There have been a load of a few thousand digit numbers added to factordb recently. When factordb tries to factor them it runs ECM, which often finds a composite factor which is the product of most of the smallish factors of the number. That's probably the source of most of the small numbers with many factors.
And the reason why there are over 121000 PRPs under 3000 digits!
Try picking a few and clicking "More information" to see what it's a factor of and following the chain. That should show you where stuff is being added now.
Chris
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