Recently I have assisted several indie authors who were having a problem uploading to Kobo after following my book instructions.
Most often the problem is in the use of the BISAC code, which is a U.S. based categorization scheme. Kobo validates epubs against the international validator. You can check it out here: http://validator.idpf.org/ Any time you get an error on an epub upload you might try validating it here first. I have found that every time Kobo has given an error when authors have uploaded epub following my book instructions, the validator indicates it does not recognize the BISAC code.
Over the past two weeks we have identified two coding problems for different distributor uploads: 1) BISAC codes for Kobo; and 2) Custom codes for keywords for Apple.
Both the BISAC code and the custom codes for keywords are accepted at Barnes and Noble and in MOBI form at Amazon.
Therefore you have two choices when setting thee two pieces of metadata for your books.
Do not include the BISAC code or the keywords custom code.
Create a separate EPUB file for Kobo uploads and a separate EPUB for Apple uploads.
The first choice may seem easier on the front end, and I have to admit that moving forward I will recommend that to most authors.
With our International distribution, it is important that we follow metadata tagging protocols that fit the most hardware options.