When Setting Recycler Efficiency to 100%, some items still disappear without any outputs.
Was this with quality modules in it, or without? With quality modules, you might lose items or get doubles.
See https://mods.factorio.com/mod/janky-quality/discussion/655c5d508a0d3fe67382a99d
If it was without quality modules, then indeed it's an issue.
About the second point:
It is expected to get possibly higher quality items when putting quality modules in the recycler, for either items with that turn to ingredients or the items themselves. Think of it as finding the 25% quality parts of a big item.