Before striking the flan was trimmed and planed with a lathe like device that left the central pit. See the link below for much more than you wanted to know. http://www.classicalcoins.com/flans1.html and 8 pages following it You could start with page 6 but you would miss a lot.
These dimples are particularly common on coins of Thrace, Moesia inferior, and Asia Minor. The mint of Pautalia, in Thrace: Marcianopolis, in Moesia Inferior: Mesembria, in Thrace: Anchialus in Thrace: Philippopolis in Thrace: Tomis in Moesia Inferior: Nicaea in Bithynia:
Interesting. I know that many early US coins have a center mark on them. Didn't realize that applied to some ancients too.
The early US coins adjusted the silver value with a plug which is a different thing than these remnants from flan smoothing. If you like plugs there are some ancients that added little plugs of gold to a silver coin (I do not have one) and several bronze coins of Aksum that placed a bit of gold in a recess on the reverse that was not a plug because it did not go through the flan.