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Going to need a sample epub (non-commercial/non-copyrighted please) and the steps to reproduce the error. There's just not enough info there to troubleshoot what might be happening.
Whatever the issue is, you seem to be saying that you have the exact same epub with the exact same version of the plugin (using the exact same plugin settings/preferences), and using that plugin on the epub in 0.9.0 will cause an error, where 0.8.7 doesn't. Is that right?
Keep in mind that if you have some regex Find & Replace going on in your plugin that relies heavily on code being formatted precisely the way the pretty-print in the Sigil 0.8.X series formatted things, then that regex very well could be broken when applying it to code formatted with the 0.8.9xx and higher Sigil's pretty-print. I'm not saying that's what's going on here, but it's something to keep in mind.
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