Is it acceptable to email the author of a paper that you cannot follow?
It's okay, and more than okay, to ask for clarifications on specific bits that you were unable to follow. Academics love talking about their work, and they love spreading knowledge.

It's less okay to email someone out of the blue and say "explain yourself better". As SolarMike said, this paper has already been peer-reviewed; people in the field have looked over it and said "yep, that looks good". It may indeed be true that the paper was not written clearly enough to be understandable to someone without extensive knowledge of the subfield, and it may also be true that a better written version of the paper would have been more widely understandable without compromising its concision or its organization, but that's not a sin the author is required to atone for.

Try reading a few of the papers that paper cites, particularly ones sharing one or more authors; authors will often introduce and explain formalisms in one paper, and then take them "as read" in later papers (either accidentally or because they see the later paper as incorporating the earlier one by reference). If you still can't follow it, definitely contact the author... but make sure your request comes off as a request, not a criticism.