It wasn't especially unusual in the mid-60s for there to be unpredictable differences between international editions of albums. This was particularly the case with British acts, as the US and Canadian licensees would usually recompile (and even re-title) albums to include hit singles omitted from the UK versions. This often led to the accidental selection of alternative versions and mixes from the pool of recordings made available to the licensees. The Beatles, The Rolling Stones, The Animals, The Yardbirds and many others suffered from this syndrome.
However, Dylan's case was different - there was no artistic or commercial reason for Columbia's subsidiaries in Canada and Europe to vary the content of the album at all. In this context, the release of Blonde On Blonde does seem to have been an unusually haphazard affair.