So, I found your error in my logs and fixed it. Hopefully you don’t see those things anymore! Please let me know if you do.
It absolutely does look like a bug. Would you mind filing a bug report in the Product Requests category? It makes tracking these things a lot easier.
That’s somewhat surprising. Now, the grading prompter doesn’t take into account when you read something (perhaps it should!), but it does prioritize prompting you to compare against like things (LN - LN, manga - manga).
Was the LN a really low level? We only consider things within +/- 5 levels of the item for comparisons, so if you only have manga around the lvl of the LN, then we may end up showing you that comparison.