This cheese can be pressed by hand into the molds almost enough for good knitting...
It's been my experience that even when using small curds and keeping the curds warm, unless there is significant weight, there will invariably be small, irregular mechanical inclusions/openings in farmstead, tomme-derivative cheeses, like manchego. There may not be very many, but even with a great curd knit, some openings remain unless you press enough. I assumed that's what Caite meant, that there were some small irregular openings. Those are always caused by an incomplete knit. And the way to achieve complete curd fusion and knit is to keep the temperature up and to press with a good amount of weight (at least 2 PSI, preferably 8-10).
Regular, round holes formed by gas during aging are another thing, but based on the description, I don't think that's what happened here.