Just lost all my coins from upgrading an epic card to level 6 and the game still kept saying level 5 like something wasn’t processing but still took my thousands of coins anyways…really TC? 
Send in your ticket. Hopefully, they’ll fix your issue.
It’s probably a delay in the server. Have you tried restarting your game? Sometimes it just happens. Back in operation 2, I was trying to upgrade my Venom Blade card from level 4 to 5 which took 10 duplicate cards. My first attempt did nothing, so I tried it again, and again nothing. Later on I noticed that my Venom Blade card was upgraded to level 5; AND I had an extra 10 duplicates and missing Scrap. Anyway it seemed like my request to upgrade the card did go through, but due to a server delay it also used Scrap to create another 10 duplicates. Bear in mind at the time level 5 was the maximum skill level, so those duplicates were useless for a while…