Normally missions don't just disappear. maybe your save or game files got corrupted. Or at some point in your campaign, there was a mod active which changed the missions. If you don't play on ironman, you could create a run.txt in your "Documents\Paradox Interactive\Europa Universalis IV" folder with the following content:
Code:
swap_non_generic_missions = yes
Then you can use the console command
run run.txt to execute that effect and get the missions for which you are currently eligible. If it was caused by a broken mod or broken installation, you would have to fix that beforehand.
Or maybe you formed Spain while having a primary culture or government form which made you eligible for other missions as well. Getting new missions while being eligible for multiple mission trees in a way which was not anticipated by the developers, causes the mission display to be broken. But in all the cases which I have seen, the missions and arrows are just in the wrong place and you can still complete all missions,