Played a 4 player FFA, 2 human, 2 AI. Started with the 2 human teamed, and the 2 AI teamed (my friend forgot to put locked teams so the AI dropped their team).
We noticed that as allies, we could not put bounty on each other. This is probably intentional, however if I want to stab my ally in the back, I should be able to put bounties on them.

Anyway, later my friend allied with one of the computer opponents. The remaining computer opponent was defeated. This left my friend allied with the other computer opponent. I could place bounty on the AI, my friend could not. However, the AI could place bounty on him, and did. So it hardly seems right that the AI can place a bounty on an ally, when the human players can not.
Overall, I think you should be able to put bounty on anyone, I'd even say yourself if you wanted to get pirates to come for capital ship experience, but that's my personal opinion. Pirates don't care about allegiances, they just want the money. So it makes sense that anyone, at anytime could put out bounties.
Of course that's a change, but the AI being able to place bounties while allied is a bug.