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I looked through select2 code and I found where was and when the bug was introduced. Coincidentally, it was in version 3.4.2 that it is the current one ckan is using. See https://github.com/ivaynberg/select2/issues/1614.
What I did was upgrade to 3.4.5. You might me wondering why I didn't upgrade to the latest version (3.4.6). Well, I tried but I got a weird error and I thought that it would be better to stick with 3.4.5.
The latest version included a lot of fixes and the interval between the latest and 3.4.5 was more than 5 months (https://github.com/ivaynberg/select2/releases). That made me think that the latest version might be not as stable as the 3.4.5 because the project wasn't being actively maintained as before.