Your course may not have imported certain variations because they contained non-standard PGN notation. For instance, the most common mistake is to leave comments or variations not closed or improperly closed, for example, 1.e4 e5 (1...e6 2. d4 {comment). Notice the missing curly bracket }. If your PGN has no such issues, the file should import correctly. If you believe your file has no issues and it is still giving errors, please contact us and we will look into it.
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However, out of a test of 1,000 variations uploaded, around 99.9% were uploading correctly in our last tests (27th of February 2017). When importing, please make sure your file uses the standard UTF-8 encoding, and not a variant (e.g. UTF-8-BOM may not work exactly how you expect, but we have tried to make it work well).