There was some discussion about alien retaliation missions before the invasion. The above comment was in the context of aggressive retaliation having been enabled. But this happens with vanilla options as well.
To prove the point, In Oct 1998, I have not shot down any UFOs and I just had "recurringRetaliation" (which, with 75 % probability, was STR_SENTRY_RETALIATION). Looking at the rulesets, recurringRetaliation has 20 % chance of happening starting from month 22. Oct 1998 is month 22 so I got it in the earliest possible mission spawn. It was Chasers, so not too bad, if you just have defenders in the base. (I've often been lazy assigning defenders on various secondary bases, but I suppose I need to step up due to these random retaliations.)
EDIT: I'll add that this can be a bit tough, because at that point you're barely getting up the radar coverage and you don't have even decent interceptors yet; and you probably haven't prioritized building defenses (mass driver defenses being the best at that point) at that point. And the alien race the RNG can is not necessarily easy.
I forgot to mention in my previous reply on the matter that in addition to Syndicate and MiB threats of direct
assault against XCOM bases, there also exists a threat coming from cults. I did have a cult attack one of my bases, when I built it in Japan to take advantage of early mudcrawler advantages in deployment against HQ.
I am not 100% positive, but there may even be a threat from hybrids.
All of those threats make a great deal of logical sense, and fit very nicely into the lore.
Note to @Solarius Scorch. If there's no hybrid attack missions currently encoded, please consider adding those into the mod.
I actually do recall aliens destroying one of my entry-lift-only bases in one experimental playthrough. But whether it was aliens proper or not -- that is a question to ponder, since the error message is probably the same regardless of race.
Note to @Solarius Scorch. If there's a way to inform player which race had destroyed the base, please consider adding this functionality into the mod.