There's a vague verse in parshas Mishpatim which is a good prototype for my question:
מְלֵאָתְךָ֥ וְדִמְעֲךָ֖ לֹ֣א תְאַחֵ֑ר בְּכ֥וֹר בָּנֶ֖יךָ תִּתֶּן־לִּֽי׃
Literally: do not delay your full and mixed things. Give me your first born son.
Rashi has his interpretation, which makes the two halves of the verse unconnected.
The explanation brought is your full things refer to a pregnant woman, and mixed things refer to man's seed. The verse is therefore interpreted to mean do not delay marriage, so you can have kids, and give your first born to Hashem. This way, the verse fits nicely as a whole. See the Ibn Ezra's issue with this interpretation, which he rejects.
However, Mahari Kara, potentially a student of Rashi, interprets the verse the same way as Ben Zuta (click here and click his name). Rav Chaim Vital, in Sefer HaLikkutim parshas Mishpatim does as well. It's not definite that either of them had seen this comment from Ben Zuta, or Ibn Ezra, and perhaps they happened to interpret the verse in the same way.
I'm looking for other examples of this phenomenon, where a Rabbinic commentator gives the same explanation a Karaite scholar does, without quoting/citing them. These would be explanations that are either known as Karaite views, e.g. quoted by Rishonim as the Karaite view, or views that are known to have been held by Karaites, and that the significant majority of classical Rabbanic expositors do not agree with. That would preclude something like וידבר ה' אל משה. (Although I don't know if that disqualifies my prototype case.)