Input languages
In the previous versions of Firefox, when selecting a language of input, all the other languages were unselected. This was a much better option than today's, where they remain selected, allowing to check in several languages simultaneously. The problem with that is that when a word exists in both languages with a small difference (accent, two letters reversed or something like that), if there is a spelling mistake, it may not appear. In the example below, "defense" should be with an accent: "défense".
Všetky odpovede (3)
You can currently select multiple dictionaries for spell checking, so in your case probably best is to ensure you only have one selected at the time to avoid confusion.
I speak enough languages to know that that'll be the case for all the languages written with the same, or almost the same, alphabet so it's a BAD "current" situation, not a good one at all. It may have seemed like a good idea (avoid having to change language) but it in fact doubles the trouble.
I don't think that there is an easy solution of how to deal with words that appear in more than one dictionary as it is possible that you would want to quote a sentence in a language other than the main language you currently use and you would have to flag words that appear in multiple dictionaries what can be quite annoying at times.