Technically it’s wrong, but it’s also right at the same time. The “ビー” part in ビー玉 is the shortened version of ビードロ (vidro), the Portuguese word for glass, and as a foreign word, it is written in katakana. However, since WK primarily expects hiragana input, it also accepts the hiragana conversion of the word.
Now why isn’t it “びいだま” then? The reason is that it is a conversion from katakana. This isn’t the only said “illegal” conversion, that is, a word that shouldn’t exist in hiragana in the first place. There are several syllables that only exist in katakana, yet they often find their way into hiragana-written words as well. That’s how we get syllables like ふぇ (fe), ふぃ (fi), うぇ (we), etc., that should not be used in the hiragana set, but in case for some reason it is more practical to use hiragana in a text instead of katakana (like in WK), then these kinds of conversions appear.
The same applies to the long vowel sign. In case we are talking about a forced katakana → hiragana conversion (like now), that sign remains in place.
Having said all that, I also kept messing up ビー玉 and used い instead of ー.