Muffler delete is a known cause of misfires. It manifests as a popping sound surrounded by the other shitty sounds produced by such a modified exhaust. We have all heard it.
A misfire is raw fuel being expelled.
A misfire is raw fuel being expelled.
But the incomplete ignition of fuel can occur in both stock and modified vehicles. My car is completely unmodified, but can very easily have a low quiet popping noise during downshifts. With e removal of my muffler, it would be quite loud.
A modified engine can do this to a much greater extent, depending on the modifications. Some do so intentionally with what is known as a "burble tune", which is quite annoying in my opinion. It is inspired by rally cars that would intentionally inject fuel during the exhaust stroke and fire the spark plugs to keep exhaust driven turbines spinning even when under deceleration.
They can lead to the popping sound you're describing, but they don't always, and they're far from the only cause, and muffler deletes aren't necessary for those either. Unburned fuel hitting oxygen in the tip of a hot exhaust and immediately burning is the direct source of the noise, and causes for that are numerous.
I saw this analyzed on a Chevy Silverado that would randomly misfire. Everything else checked out: fuel pressure, spark plugs, firing timing, and fuel injector pressure. The remaining item: muffler delete.