This is WAD (Working As Designed).
It tells you the total gems you have recieved from the level, not how many you just received this time around.
Normally, I’d tell you to search before posting, but sometimes it might be hard to figure out exactly what to search for… Oh, that wasn’t so hard after all, so Please search before posting. 
I searched on “gems” and one was on the first list.
http://discourse.codecombat.com/t/problem-only-1-2-of-promised-gems-added-to-gems-counter/3741
clicking more gets:
http://discourse.codecombat.com/t/gem-problem-replayable-levels/3748
http://discourse.codecombat.com/t/incorrect-gem-awarding-on-defeating-backwoods-brawl-multiple-times/2637
Searching on “repeatable” or “sarven siege”
http://discourse.codecombat.com/t/not-getting-full-rewards-in-repeatable-levels/3376
etc