I haven't tried it myself, but the code trigger should stop that with the "NOT = { has_modifier = lithoid_crater".
Shout if you still has the problem, if you do I can add
NOT = { has_deposit = d_lithoid_crater } to the trigger and see if that stops your bug.

#Lithoid origin
planet_event = {
id = origin.3010
hide_window = yes

is_triggered_only = yes

trigger = {
exists = FROM
FROM = { is_ship_size = lithoid_colonizer}
NOT = { has_modifier = lithoid_crater }
}

immediate = {
add_deposit = d_lithoid_crater
add_deposit = d_buried_lithoids
add_deposit = d_buried_lithoids
add_modifier = { modifier = lithoid_crater }
}
}

Having done something like this when the lithoids came out, I have to ask, have you tested what happens when you colonise a world, remove the colonists and abandon it all, then recolonise. Do you still get multiple craters, and a stacking penalty to habitability?