@Karthick can you download and try this measure on your model. https://github.com/UnmetHours/openstudio-measures/tree/master/surface_matching_diagnostic (You can clone this repository, or download zip of the entire repository, which is just a few measures). I can also directly mail a copy of the measure. Note that this will be slower on large models than the standard surface matching measure.

It is a special version of our service matching measure that does a number of additional features.

• It looks for duplicate vertices in a surface
• Duplicate surfaces in a space
• Mirrored surfaces in a spase
• It removes collinear vertices in a surface (this is what I think is affecting your simple use case)

Beyond this it also does surface intersection and matching on a single pair of spaces at a time. This is helpful when surface intersection is crashing to identify the specific space combination that is an issue.