Science

I've checked a few newspapers in Spanish (El Heraldo, El Deber*, Clarín), and the total number of votes seems rather consistent with what the article linked in the OP says. Based on that I think that the hypothesis in the P.P.S. (sloppy post-processing) is probably incorrect, as multiple independent sources wouldn't be likely to retrieve the info from the same intermediary.

IMO the simplest explanation is the implicit main hypothesis (someone makes up the percentages, then apply them to the total # of votes, then round them down to the nearest integer). As in: fraud. Fairly common in the Americas in general, not just in Venezuela, just a bit too blatant for the traditional modus operandi (that involves stuff like: finding bullshit reasons to not count some urns, your grand-grand-grandma coming back from the grave to vote on your candidate, etc.).

*El Deber lists the wrong percentage for Urrutia, 42,2% instead of 44,2%. This looks like a typo, given that the total number of votes (4.445.978) is consistent with the other sources.