At one point I volunteered to join an anti-jihadist Syrian militia (YPG) that was backed by the US government. When I returned to the US, they flagged my passport (and interrogated me everytime I crossed a border for about a decade).... thinking I was a jihadist.
So yeah consider that the government is so dumb that one half of the government thinks the secular anti-jihadist militias supported by the other half of government are actually jihadists.
They don't care about that. They care about the fact that you now have irregular warfare experience. Their morals are wholly situational, so they assume the same is true of everyone else.
It's not a terrible assumption; if you study extremist circles for long enough you come across examples of people who completely flip sides because they were only ever in it for the extralegal opportunities. Of course, you can find similar chameleons in politics.
So yeah consider that the government is so dumb that one half of the government thinks the secular anti-jihadist militias supported by the other half of government are actually jihadists.