Yes! I always ask the editorial office: "Hi there, your pdf is broken, captions are separated from legends! please fix." Sometimes they get back to authors and produce a sensible manuscript -- @PLOS is one of the worst offenders.https://twitter.com/magnusnordborg/status/930796448555421697 …
It's funny - I actually prefer the figures being at the end. That way I can have them separately so I can get to them quickly whenever they're mentioned in the manuscript.
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I am not dogmatic about in context/at the end. But it drives me nuts if legends are separated from figures.
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