Errant black boxes on layers

Hi MarkColomb I'm not sure I'm seeing what you are seeing. Maybe a different browser? This is using preview which is Chromium. The only issue I see is that the items that have been highlighted, remain highlighted which can cause the highlights to overlap. Also, the highlights did not all have the same animation on them. I also noticed some of your highlights are Storyline shapes and some are SVG images. I would recommend you change them all to Storyline shapes so you can update the style easily.

I've added a suggestion here (B.O.M and Note block), just based on accessibility/usability. When using a highlight over the top of the element you are highlighting, it can actually have the reverse affect and make it more difficult to read. I wouldn't recommend using an semi-transparent colour in the shape. Just go with a strong border colour. The pulse animation also grabs the attention of the eye better than the fade.

Just suggestions. Disregard as necessary.