Now and again I see strange situation with my harmless explorer scouts.

1. I am entering hostile system with the enemy troops. I am receiving "You was attacked", and I am selecting "Flee", of course. I have no weapons anyway.

2. Right after that I receive message about "You have enemies near" with the option to attack! I am selecting "Do nothing", of course.

3. My ship is fleeing.

If there are no troops, it's normal #2 only, of course. But is it something wrong with sequence of #1 and #2?

I can confirm this is working by current design.

#1 - AI fleets has option to attack first (unless you have 'Engage Sector' selected before pressing turn). If they do attack, prompt option to engage or flee.
#2 - Player then has their turn with prompt option to attack or do nothing (continues to flee in this example).

I think what you are saying is player shouldn't need #2 prompt because it has no weapons to attack.

Aha. Seems wrong for me then.

No, it's not about weapons. It would be foolproof with removing option, but I don't think it's crucial (still useful. I wrongly "attacking" scouts with disarmed invasion ships that way now and again. Hmm, it deserves another suggestion - will do.)

Problem is, if my ship is fleeing already, it must not have chance to attack. Only defend.

Also, interesting question: if I am by chance will win the battle during fleeing, will I continue to flee? Outcomes looks wrong both ways (why to flee, if I am winning? Why to stop fleeing, if it could be totally different troops?). So disabling attack order altogether for "fleeing" ships seems most logical decision for me.

Noted, I agree it makes sense that if fleeing it should not prompt, sound logic. Thank you.

I am almost sure that you noticed it, but to be sure, I'll emphasize: you must have ability to fight back, if you attacked, and it will not cancel "fleeing" order, otherwise it would be not fair.