Now the problem since that event : i'm near 3 months into my space marine run but since that enemy ship , i have not seen anymore of them of any kind, so far the game is repeated non stop chaos cult alert (those summon/sacrifice things), with sometime a terror mission alert filled with chaos troops between them.
But absolutely no ship in those near 3 months . Is that a bug or is it part of the gameplay that ships are so incredibly rare ?
Now another question, probably not a bug but something i can't figure out : in my base when i want to build facilities, only half of them can be selected, the bottom half (trade outpost, training facillity, clear terrain, etc...) are present but clicking on them does nothing, they just can't be selected, why is that ?
Have you built more bases with radar facilities? Most likely the UFO missions are happening where you don't have radar coverage. You can see roughly where the missions are happening by checking the Graphs menu from the main Geoscape screen.
If you're getting a lot of cultist alerts, that means there are cultist bases in the area. You can find them by patrolling with your craft (there should be an article about this in the Assistance category of the Codex).
There are two types of bases you can build, determined by the kind of access lift you use. The initial base is an underground one with the majority of facility types, then you can choose to build either more underground bases or above-ground outposts, which is what the disabled facilities are for.