Is this happening to anyone else?

I only have one more spot in the neon district that I have not completed the side mission on, and it is a side mission where you protect the medical clinic.  However as soon as I step into the neon district, the side mission disappears! but as soon as I go to another island, the mission will reappear.  It seems like there is a magic spot where this mission will activate and disappear.  I kinda want to control all of the neon district but this glitch is keeping me from doing it.  Anyone have any ideas what I should do?

No idea. If it's a side mission showing up on the map it should be there when you encounter it. Some of the side missions are "hidden" and require you to kill an enemy before you unlock it. From that point you'll get a piece of paper showing you the location of a package, which you'll have to find. Those missions don't show up on the map.

Have you tried going to the clinic anyway and seeing if you can interact with mission starter?

I think missions disappear when there are enemies around the area, or if the quest giver got knocked down. If it isn't those then I have no idea.

Thanks a ton guys.  I will go check out whats going on.

Either that, or you have to kill a few enemies to see if the side mission drops where you have to find whatever the guy you killed hid and where.

No it was where enemies were killing the side mission giver, and then the whole mission would just disappear.