What do you mean by holes, exactly? Sharp, precise openings or soft indentations? If the latter, it could be a case of sinkmarks, where the plastic has sunken in during the injection process.
It usually results from poorly-engineered injection moulds, exacerbated when the mould was inadequately heated (a variant is the ejector pin mark) and was very common back in the day when injection kits generally had greater material thickness. Still happens a lot on short-run kits, but I've also seen state-of-the-art items where it happens.
Here's a professional's article on the issue:
https://www.engineersrule.com/not-sunk-deal-sink-marks-injection-molded-part/IIRC, the plastic on the surface cools quicker than within the piece, which may lead to a localised collapse. Alternatively, the mould wasn't filled completely - I recently bought one of Revell's brand-new M109G kits which was missing a roadwheel support arm.