This can happen when you change the time signature earlier in the flow than an existing time signature or barline (like a double barline or normal barline with a red signpost to show it’s been added explicitly).
So for proofreading beats in bars, your key places to check are:
- The bar before time signatures
- The bar before unusual barlines
- The bar before barlines with red signposts
To fix it: either insert beats (eg using the bars and barlines popover) or reinput the previous time signature with Insert mode active.