ご返信ありがとうございます。マスターデータの件ですが、確かにおっしゃられるとおりに件数が１件足りませんでした。修正いたしましたが、やはり不具合は改善されませんでした。

改めて調査を行ったところ、以下のようなログが見つかりました。問題点はこちらだったようです。申し訳ございません。

[2020-05-04 14:30:14,248743] eccube.INFO [63118482] [a67fb60a] [2] [LogListener:logResponse:96] - < 200 [GET, /shop/xxxxx/setting/system/log, xxx.xxx.xxx.xxx, https://xxxxx/xxxxx/setting/system/masterdata/Eccube-Entity-Master-OrderStatusColor/edit, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:14,191058] eccube.INFO [63118482] [a67fb60a] [2] [LogListener:logRequest:83] - > GET /shop/xxxxx/setting/system/log [GET, /shop/xxxxx/setting/system/log, xxx.xxx.xxx.xxx, https://xxxxx/xxxxx/setting/system/masterdata/Eccube-Entity-Master-OrderStatusColor/edit, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:14,182606] eccube.INFO [NULL] [a67fb60a] [NULL] [RouterListener:onKernelRequest:145] - Matched route "admin_setting_system_log". {"route_parameters":{"_controller":"\\Eccube\\Controller\\Admin\\Setting\\System\\LogController::index","_route":"admin_setting_system_log"},"request_uri":"https://xxxxx/xxxxx/setting/system/log"} [GET, /shop/xxxxx/setting/system/log, xxx.xxx.xxx.xxx, https://xxxxx/xxxxx/setting/system/masterdata/Eccube-Entity-Master-OrderStatusColor/edit, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:14,081404] eccube.WARNING [NULL] [a67fb60a] [NULL] [Application:loadPlugin:993] - Service provider class for plugin OrderStatusColor not exists. {"class":"\\Plugin\\OrderStatusColor\\ServiceProvider\\ServiceProvider"} [GET, /shop/xxxxx/setting/system/log, xxx.xxx.xxx.xxx, https://xxxxx/xxxxx/setting/system/masterdata/Eccube-Entity-Master-OrderStatusColor/edit, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:09,508041] eccube.INFO [63118482] [1cc71bb4] [NULL] [LogListener:logResponse:96] - < 500 [GET, /shop/shopping/complete, xxx.xxx.xxx.xxx, https://tdpa.nekonet.ne.jp/tk/3d_auth_res, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:09,505573] eccube.CRITICAL [63118482] [1cc71bb4] [NULL] [LogListener:logException:112] - Doctrine\ORM\ORMException: The identifier id is missing for a query of Eccube\Entity\Order (uncaught exception) at /xxxxx/vendor/doctrine/orm/lib/Doctrine/ORM/ORMException.php line 259 {"exception":"[object] (Doctrine\\ORM\\ORMException(code: 0): The identifier id is missing for a query of Eccube\\Entity\\Order at /xxxxx/vendor/doctrine/orm/lib/Doctrine/ORM/ORMException.php:259)"} [GET, /shop/shopping/complete, xxx.xxx.xxx.xxx, https://tdpa.nekonet.ne.jp/tk/3d_auth_res, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:09,455650] eccube.INFO [63118482] [1cc71bb4] [NULL] [LogListener:logRequest:83] - > GET /shop/shopping/complete [GET, /shop/shopping/complete, xxx.xxx.xxx.xxx, https://tdpa.nekonet.ne.jp/tk/3d_auth_res, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:09,450813] eccube.INFO [NULL] [1cc71bb4] [NULL] [RouterListener:onKernelRequest:145] - Matched route "shopping_complete". {"route_parameters":{"_controller":"\\Eccube\\Controller\\ShoppingController::complete","_route":"shopping_complete"},"request_uri":"https://xxxxx/shopping/complete"} [GET, /shop/shopping/complete, xxx.xxx.xxx.xxx, https://tdpa.nekonet.ne.jp/tk/3d_auth_res, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]
[2020-05-04 14:30:09,440146] eccube.WARNING [NULL] [1cc71bb4] [NULL] [Application:loadPlugin:993] - Service provider class for plugin OrderStatusColor not exists. {"class":"\\Plugin\\OrderStatusColor\\ServiceProvider\\ServiceProvider"} [GET, /shop/shopping/complete, xxx.xxx.xxx.xxx, https://tdpa.nekonet.ne.jp/tk/3d_auth_res, Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36]


後者のデバッグモードのエラーのログはこちらでしたでしょうか？

INFO - skip AnywhereProductInfo event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/AnywhereProductInfo/event.yml"}
INFO - skip ProductMetaCsv event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/ProductMetaCsv/event.yml"}
INFO - skip Recommend event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Recommend/event.yml"}
INFO - skip SalesReport event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/SalesReport/event.yml"}
INFO - skip Securitychecker3 event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Securitychecker3/event.yml"}
INFO - skip Shiro8NewProductBlock3 event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Shiro8NewProductBlock3/event.yml"}
INFO - skip AnywhereProductInfo event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/AnywhereProductInfo/event.yml"}
INFO - skip ProductMetaCsv event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/ProductMetaCsv/event.yml"}
INFO - skip Recommend event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Recommend/event.yml"}
INFO - skip SalesReport event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/SalesReport/event.yml"}
INFO - skip Securitychecker3 event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Securitychecker3/event.yml"}
INFO - skip Shiro8NewProductBlock3 event.yml not found.
Context: {"path":"/xxxxx/app/Plugin/Shiro8NewProductBlock3/event.yml"}
WARNING - Service provider class for plugin OrderStatusColor not exists.
Context: {"class":"\\Plugin\\OrderStatusColor\\ServiceProvider\\ServiceProvider"}
INFO - INIT
INFO - Matched route "yamato_shopping_payment".
Context: {"route_parameters":{"_controller":"\\Plugin\\YamatoPayment\\Controller\\PaymentController::index","_route":"yamato_shopping_payment"},"request_uri":"https://www.kuriyamaen.jp/shop/index_dev.php/shopping/yamato_payment"}
INFO - PROCESS START
Context: ["yamato_shopping_payment"]
INFO - > GET /shop/index_dev.php/shopping/yamato_payment
INFO - LOGIC START
Context: ["yamato_shopping_payment"]
ERROR - Symfony\Component\Debug\Exception\ContextErrorException: Warning: count(): Parameter must be an array or an object that implements Countable (uncaught exception) at /xxxxx/app/Plugin/YamatoPayment/Form/Type/RegistCreditType.php line 132
Context: {"exception":"Exception(Symfony\\Component\\Debug\\Exception\\ContextErrorException): Warning: count(): Parameter must be an array or an object that implements Countable"}
CRITICAL - Symfony\Component\Debug\Exception\ContextErrorException: Warning: count(): Parameter must be an array or an object that implements Countable (uncaught exception) at /xxxxx/app/Plugin/YamatoPayment/Form/Type/RegistCreditType.php line 132
Context: {"exception":"Exception(Symfony\\Component\\Debug\\Exception\\ContextErrorException): Warning: count(): Parameter must be an array or an object that implements Countable"}
INFO - LOGIC END
Context: ["yamato_shopping_payment"]
INFO - < 500
INFO - PROCESS END
Context: ["yamato_shopping_payment"]

何度もお手を煩わせて申し訳ありません。どうぞご教示くださいますようお願い申し上げます。