Yes, they do. If you are lucky you can localize them with a magnetometer (20 years ago I did this walking through the bushveld, now this is also done with helicopters). If you miss one you may be out for a bad surprise. Whereas in an opencast mine you just blast the whole stuff and pick the coal out, in an underground mine a dyke may provide a much darker outlook: A 2007 study for the EU "COAL OF THE FUTURE" has a few more details (currently offline):
"In southern African mines the coal seams are heavily intruded by Jurassic dolerites dykes and sills. These either burn the coal or cut through it and due to their hardness and possible seam displacements, which makes mine planning difficult.
The presence of these intrusives is the main reason why so few long wall or short wall mining methods are used in South Africa."

This makes mine planning even more complex than they are already: Unlike the regular (although folded) coal seams we are used in Europe the South African seams I have seen were much more irregular due to a different deposition history. It was quite hard for me to keep the track and I was impressed of the local geology team who managed it regularly.