Two new games coming from Arcen! Exodus of the Machine!And Skyward Collapse!
Probably you've run into a black hole machine on that planet -- if you kill it, you can then have your ships escape.
They shouldn't be invisible unless you're playing against something with a planetary cloaker, or perhaps the camouflager AI type.
I'm really not sure what's going on, it doesn't sound like they are really hidden. Are they just not showing up on the planetary summary sidear? In that case, you just need a scout with you.