I think it could be troubling depending on why those stoppages occurred in the first place. If they were due to operator error (which is possible given that most troops prioritize rifle training over pistol training) or poor maintenance (which is likely, especially given how old and abused some of those M9 components were) then I don't necessarily find that to be a "troubling" fault of the firearm. Any firearm needs proper maintenance (to include parts replacement/servicing) in order to stay reliable over the long run.
FYI, a former Army armorer gave a very good explanation of why that perception existed among certain troops:
As someone who carried and shot the M9a1 quite a bit, I observed that design to work just fine...but weapons maintenance and training can vary quite a bit in one branch from the next.
Perhaps, but if you honestly think there will be the potential for any sort of conflict within the wire, you're going be walking around with your rifle. And that's exactly what everyone did, at least on the COP's that I was at...excepting a few officers and admin types here and there.