Recently, I finished up the Deathclaw Promontory for the Enclave power armor and after using Brotherhood armor to repair it NCR aligned places have been trying to kill me. It's as if the game never registered that I wasn't wearing Brotherhood armor anymore.

I think I solved the problem by switching back and forth between faction armor.

It seems they are also targeting Veronica.

No it doesn't make NCR hostile but you identified the real cause.

When you repair a suite of armor using a suit of faction armor your wearing the game never registers that you removed it. And thus switching faction armors solves the problem. THE EXACT same thing happened to me when I first got that armor.