Yes, I mean things like OE, or possibly others diseases caused by different types of viruses and microbes. Not everything is known about diseases in monarchs/butterflies (or humans, for that matter, where we spend trillions on trying to know).
If your collecting from wild, you won't get inbreeding. If you have pesticide problems, the larvae would never make it to pupa.
It really sounds like you've had tachinid + other parisitism (microbial, maybe OE).
Next year, try a couple batches of maybe six or so eggs, each batch from a different part of the county in which you live. Keep them isolated and feed each batch a different kind of live milkweed. Keep the whole plant(s), eggs, and larvae inside a screened enclosure with no other insects present. I almost guarantee you will not have so many deaths this way. Don't try and keep to many larvae in the same small volume of space. Also, don't keep the cage in a damp, musty environment.
I don't mean to sound like a know-it-all, I'm definately not. But this is what I have been doing for the 2nd year now, with 100% health rate.
You'll have better luck next year!