The tomlkit parser rejects the following document:

[[fruit]]  # the issue disappears if [fruit] is a table instead of a table array
apple.color = "red"

[potato]  # the issue disappears if this line is removed

[fruit.apple.texture]
smooth = true

and raises:

tomlkit.exceptions.ParseError: Key "fruit" already exists. at line 7 col 0

It seems clear to me that the document is valid TOML 1.0.0. In any case the presence of the [potato] table should not make a difference wrt its validity.

This issue applies to the latest commit 6512eaa on master as well as the latest release v0.11.6.

I'm experimenting with a TOML fuzzer which revealed this issue. I guess most normal applications are not likely to hit this case, so I understand if this gets low priority. It still seems worthwhile to fix it though.