I have seen that in 2 scenarios.
1. You print beyond the finisher abilities (600 pieces of paper and you tell it to staple the whole thing together)
2. The Freeflow HDD is full (ish)
Of course these are not the only causes, but they are the most common I came across working on Light Production RIPS
If you don't have a RIP, the integrated controller has Memory settings, I would suggest setting it to spool LPR/LPD jobs to HDD. Which should be found as admin by going to Machine Status > Tools > System Settings > Print Service Settings > Allocate Memory (Wording may not be exact, I am referencing from a similarish Fuji Xerox based controller as I don't have a D95 in my lab)
The basic gist of it is that documents will randomly print out with half of a job correct with staples/hole punches, and then the other half (or smaller portion down to even two pages) will print out incorrectly. Usually the incorrect portion is very similar to the settings of the first half, but things like no staples, two hole punch instead of three hole punch, or hole punches on the wrong side seem to occur. Other things that have happened is two pages out of a single print job printing duplex instead of single-sided, but I can't imagine any way to program that. I've spoken with a Xerox technician and re-initialized a lot of settings, but we're moving onto the possibility of a power surge or inconsistent power outlet causing corruption and other issues.
Anyone ever experience anything like this? We're going to monitor the power situation for two weeks, but any suggestions would be extremely appreciated. This issue is driving me nuts, because it happens around once per week and it's just like the printer forgets what it was doing in the middle of a print job and tries to correct itself before making small mistakes.