No.
The rider can be disqalified after the race, if there is a problem with the bike. Like in Japan, moto3 rider has been dq'd due to weight of the bike (too low).
And if there is an incident between two riders, and one continues the race. If this happenes early, rider can get "ride trough" penalty or worst case, he gets a black flag. But if it happenes in last 2 laps, there is no time for other penalty than additional time. So rider recives 30 seconds to his race time, which surely puts him outside points. Like Zarco in Silverstone after a crash with Lowes.
I've never seen points being taken away later than the same day.
But riders can get points for irresponsible driving. When/if you colect 4 points, you start from the back of the grid. Same goes for 8th engine used in one year (for Honda, Ducati, Yamaha and now Suzuki) and for breaking other engine rules, happens a lot in moto3.