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I have had this problem before and have tried several possible solutions.
1) run the intersect in entire model measure again from within the Sketchup plugin (or try only running it for only the zones you are having trouble with and see if that works). Sometimes I will try it for two adjacent floors at a time and this minimizes the problem.
2) run the measure from within OpenStudio to intersect in entire model and then open it again in Sketchup.
3) manually try deleting the extra lines or redrawing the trouble surfaces, the run either the interest or surface match measures again.
Usually for large buildings I can get the majority of the surfaces to intersect and match without trouble, and have to go back and manually fix about 3 surfaces that probably weren't drawn correctly. Here are some similar questions on the forum:
https://unmethours.com/question/2382/intersect-feature-creates-subsurfaceswindowsskylights/
https://unmethours.com/question/1116/after-intersecting-the-entire-model-and-surface-matching-only-a-few-spaces-interior-spaces-show-up-green-whats-going-on/
https://unmethours.com/question/909/surface-interaction-and-match-problem/