I agree with you about being skeptical here. It appears that this was likely just someone who screwed up. I doubt it was a conspiracy or intentional. In fact, both parties ended up suing to keep polls open:

As ballots ran short, groups filed two lawsuits to try to give people more time to vote Tuesday night. One was filed by the nonpartisan group Mississippi Votes, and the Mississippi Republican Party initially supported it. The other was filed by the Mississippi Democratic Party.