I did notice this but decided it wasn't so bad, the transposers are able to pick up the things that fall into small holes, just not the deeper holes. I figured an easy way to solve this would be to have yet another shield projector that makes a small lip in front and 1 block below the line of transposers.
Again though, I don't think it matters much, I let this machine run for a while and then checked how many entities there were on the ground and it was less than 400 at all times.
Thanks for the comments guys, I really appreciate it! I'm always trying to figure out new builds so If anyone has an idea for an interesting build let me know!