Okay i was just playing a game vs. some AIs and i've noticed that creep health is not what it should be, so i did some testing. It turned out that i'm not blind or mad and there is really a bug with valor flag.
The test games had all settings set to default, opponent was one easy AI and map was Cataract.
I mostly didn't buy any citadel upgrades, i have only tested with and without the first level of creep health upgrade. Either way the bug happened, only with different health(obviously).
Here are some pics:

This is starting health of minotaurs at Cataract.

This is buffed health of minotaurs after capturing enemy Valor flag.

And this is what happens with the new wave(and all upcoming) of reinforcements after the enemy captures Valor flag back.