I recently hit a player who had hit me, that player then jumped to a larger more powerful legion and alerted me there. I feel that the alert should not be carried over to the new legion, this just sets up a bait and hit type issue. I feel that is why he hit me hoping for a response from me, his legion has several players who are higher levels than I. Is there something that can be done that would prevent this from happening?

You can jump to a even better legion and alert him...see how he likes it...maybe he was just trading and happen to get to that legion and decides to alert you

That just seems too conveniant...
Not sure if it applies to pvp alerts but there is a 24 hour alert period. How long between you hitting him and him alerting you?

Exactly. I seem to have missed this thread earlier. You can only alert someone who has disabled/raided/hacked/invaded/trap-tripped/arti'd you within the last 24 hours. Upon joining a new legion, you have a 24 hour cooldown before you can alert an enemy ship. This was done so you COULDN'T alert someone in a new legion UNLESS they do something to you after you join. SO, unless you do something further to the guy AFTER he joined the new legion, he can't alert you. If he was able to alert you in the new legion, you did something to enable him.