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If the problem occurs intermittently, then it's important to figure out under what conditions does the problem occurs. What is unique about the times the error occurs, such as is it always the same query or same data that produces the error? Figuring out the commonalities is key.
My guess is that this problem may more likely linked to Oracle Spatial than ODP.NET. I'm not saying there is a bug in Oracle Spatial necessarily. There could be some application-specific data or design issue. It's just that this type of error is likely to be encountered more often within a generic Oracle Spatial app than an ODP.NET app. You may have more luck if you ask this question on the Oracle Spatial forum if you don't resolve the question on this forum.
Oracle Spatial Forum:
I've seen that specific error before with a geometry that Oracle Spatial thinks is invalid. Does it fail reliably for a given query? If so, you'll need to look at both that specific query and the data in the table to figure out where the invalid data is.
If that query works sometimes but not other times with the same data in the table.. yeah, that's weird.