I had issues earlier today of not being on the same server as my friend in my team. We'd both go to the same area & be in different "instances". It's quite frustrating when you want to play together. Most times, one of us leaving & coming back would fix it, but one of the missions would not let us in together at all.
If you guys find yourself being in different instances, there should be text bellow your friend's name indicating the number of the instance. All you have to do is open up the map, and there is a Change Instance button right at the bottom. Indicate your friend's instance number and you're together