It bugs me when people say “the thing is is that” (if you listen for it, you’ll start hearing it… or maybe that’s something that people only do in my area.) (“What the thing is is that…” is fine. But “the thing is is that…” bugs me.)
Also, “just because <blank> doesn’t mean <blank>.” That sentence structure invites one to take “just because <blank>” as a noun phrase which my brain really doesn’t want to do. Just doesn’t seem right. But that sentence structure is very common.
And I’m not saying there’s anything objectively wrong with either of these. Language is weird and complex and beautiful. It’s just fascinating that some commonly-used linguistic constructions just hit some people wrong sometimes.
Edit: I thought of another one. “As best as I can.” “The best I can” is fine, “as well as I can” is good, and “as best I can” is even fine. But “as best as” hurts.
One thing I try to avoid when I’m writing is when two words repeat. Kind of like your example “the thing is is that.” If I catch myself writing it, I try to rearrange the sentence.
Although a pretty extreme example tickles me: “The cookie he had had had had no effect on his appetite.”