It's not really an error. It's an unfortunate side effect of the two applications working differently.
Are you talking about equations that are in paragraphs by themselves or ones that are mixed in with text?
The former are easy to fix -- you just have to define the paragraph style to be autoleading (PM automatically switches inline graphics to autoleading on import, which used to really annoy me; ID doesn't).
The latter is more difficult to deal with but I do have some ideas. If they're relevant to your situation, I explain them.