I mean; we have seen forerunner tech malfunction... Like when mendicant Bias turned against the forerunner and became a bad guy, or like when we exploded a halo (a pretty serious malfunction). or like the fact that there even was a containment breach on Delta halo at all, or like the fact that there were flood on a shield world in Halo Wars. Forerunner tech is by no means infallible.
However, you do bring up a point I hadn't thought of before; perhaps it is a piece of installation 04 or even one of the petal sections from the ark that was flung through the ark portal; or perhaps it was the ark's slips-pace drive that malfunctioned and not the halos.
Given Frankie's wording, I would be remissed if the event was something purposeful and caused by 343GS; especially given the fact that shooting part of a halo onto a random colony planet seems to have very little to do with finding the librarian