Matt patches, or 'sunken' areas, could be caused by one or more things-
1. An absorbent ground that sucked oil from the paint into the surface and left the paint dry. This 'sinking' can be prevented by using a sized (sealed) surface, a less absorbent ground or an oil ground.
2. Using very dry paint - not using an oil painting medium to add fat. This can be prevented by following the fat over lean rule and adding a smidge more oil or oil medium to each layer.
3. Using artist quality paints - because these allow each pigment to have its own characteristics and some, like earth colours, dry naturally matt. So you will have an uneven sheen when the painting is dry. This is not an error, there is no need to prevent it. Some artists like this look and so do not varnish. Other artists add a bit of oil to their earth colours. Others just even it all out with a final picture varnish. One of the purposes of a final picture varnish is to even out the sheen of a painting - you can choose matt, satin or gloss, they will all add depth of colour.
Some people use retouching varnish to fatten the sunken areas, but it is not recommended. It’s best to construct the painting well, rather than try to compensate afterwards. Retouching varnish is just diluted varnish, so it does not add the missing fat anyway.
There are those who like or dislike the practice of oiling-out. It can be useful. It is a way to add the missing fat.