I seem to be running into many limitations with either M3E, my flight planning, Lightning, or ODM itself.
I have the 3000 image tier of Lightning but it doesn’t seem to be able to handle more than 2000 images at best. And there are a lot of failed processing attempts.
Often resizing from 96dpi down to 72dpi will result in success.
Typically I use 80% or better overlaps, combined with oblique images.