SVG exported from Illustrator displaying with random black fills when imported to web app

Hello, 
I recently used Illustrator to create an SVG system map. It has many layers and paths with various fills. The problem I'm having is that we experienced some class collisions with other SVGs  created similarly using internal CSS, so we changed everything to inline. ALL of the other SVGs imported and displayed properly, but the system map had five large paths filled with black. This fill is not inside the path as it overlaps all paths that should be displayed in front of the affected path. When changed back to internal styles, with no other alterations to the graphic or procedure, it displays as expected. Can anyone explain why this is happening? We are loathe to have to keep saving SVGs with different CSS methods.