Only a guess without the document.
Go to Tools
>Chapter Numbering
.
In Position
tab, you probably changed Numbering followed by Tab stop
to Nothing
for level 2 at least.
In Numbering
tab, see if Separator Before or After contains a dot and remove it (again at least for level 2).
By the way, if your Heading 2 should be separated from preceding and subsequent text, it is much better to include this vertical spacing in Indents & Spacing
tab of Heading 2 instead of using empty paragraphs. You are then guaranteed taht absolutely all your Heading 2 will exhibit the same vertical spacing (no chance to forget the top or bottom spacing) and you can tune this spacing from a single location for immediate change over the whole document.
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