I am trying to figure out what end of round effects would be considered if they are chosen by a player.

For example, let's say I have an agenda card that lets me move troops at the end of a round. Also at the end of the round there is an ability for a rebel figure to move granted by a specific mission rule.

Which effect happens first? It seems like the latter is both a mission rule and an effect triggered by the rebel since they chose to do it.

Mission rule is a mission rule, all mission rules with end of round timing happen first. If there are more than one, the imperial player decides their order.

End of round effects from agenda cards or deployment cards are imperial effects, so they happen next.

I don't remember any rebel end of round effects. (In the campaign)

Is this from Return to Hoth? Even if the mission rule gives a choice to the rebel player, it is still a mission rule. Giving a choice does not make it a rebel ability.