If you change the appearance of a guide or hotspot manually while working on Chrome extension, they are considered as retouches.
And, retouches can override the functioning of the theme that is designated to a guide. Because they have programmatic superiority over themes.
That's why, the best practice is to change the theme of a guide rather than changing its design step by step.
If you detect any imperfection in your guide and hotspot designs, this kind of practice could be the reason behind your issue.