No it doesn't emit false positive warnings when using lists. That is FUD. But if a function explicitly requires fixnums, and you pass something of type t, it might warn (depending on the optimize settings).
In that case, everything extracted from a list is T and you'd have to get that warning you mentioned above.
Such warnings would very likely be false-positive, unless Common Lisp programs are buggy as hell most of the time—assuming that would be the real FUD, no? Therefore, the non-FUD conclusion is to expect a high rate of false-positive warnings in typical list-using programs.
TBH, I suspect those false-positive warnings you mentioned aren't bona fide warnings, but some kind optimizer stream-of-consciousness log stream.