It happened when there were several "very large" undeads in there. It did not seem to seriously impact its lethality though. (Lighter carts can stagger the creature, and then subsequent hits are unblockable, because the creature is staggered.)
Be aprised that some times sturdy undeads can make up to the door while still alive, so the potential for them to escape exists. My micromanagement prevented that, because I would lock the door when there was a batch in for "processing".
If you truly want to fix it, you will have to re-designate one of the insert-points as a track stop, (WITH THE LEVER OFF!!), and then have the dwarves load it, and push it-- then delete the trackstop. The cart just has to be on the track so it can be moved when the on lever gets pulled. I did not consider it a worthwhile thing to worry about, after noting that even huge undead still died with empty carts.
Basically, the huge undeads could go "You hit me!? WRAAR!" and throw the cart (which makes it derail, and spill its contents). However, the only place for the cart to land is on the powered track, which then sends it careening back on a collision course with the huge undead, and whammo all over again. Meanwhile, immediately after it tossed the first cart, the next one hits it, followed by the next, etc--- sending the creature flying, or making it get stunned. When flying or stunned, the creature cannot block, and all the hits land. This continues relentlessly until the big thing gets pulped. Occasionally, I noted that the undeads could block the carts, but then when they try to toss the cart (or move, allowing the carts to get momentum again), they send it on an active bit of circuit, causing it to crash into the back of the hung-up cart chain, making the stopped carts slam into the creature, stunning it long enough for the rollers to shove the stuck carts over the stunned creature, and then "THUMP THUMP THUMP", and the whole death machine winds back up again.
The smaller undeads just get clobbered without any of the interesting interactions.