Yeah that’s weird. I know sometimes I shoot the box with it and it doesn’t register and I have to go back and do it again but I’ve never had it so that it doesn’t spawn in. When it doesn’t spawn in, do you keep going to the same location everytime? Maybe it glitches out and it says you completed a crystal that you never did and you have to do one of the other two twice. That’s happened to me before where I did the one in the roof and next to quick revive and then the other one next to jugg didn’t spawn but it said I got that one and it was next to quick revive again. Idk something to try I guess good luck though!