If you change the appearance of a Guide or Hotspot manually while working on Chrome Extension, they are considered retouches.
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And, retouches can override the functioning of the theme that is designated to a Guide/Hotspot because they have programmatic superiority over themes. 

That's why the best practice is to change the theme of a Guide/Hotspot rather than changing its design step by step. 

If you detect any imperfection in your Guide/Hotspot design, this kind of practice could be the reason behind your issue.