You're suffering from 'PCB supplier that thinks they know best' syndrome.
It's not unusual for suppliers to make minor changes to a board. For example, if you have extremely thin slivers of solder mask between pads, then they can be quite legitimately removed by the board manufacturer. They'd never fabricate correctly anyway, and if a loose sliver of solder mask breaks off the board and onto a pad, it can cause a fault.
You don't, though, and adding solder mask where you've clearly specified that there shouldn't be any, is a complete no-no. I hate it when board suppliers do this kind of thing, there's no excuse for it. It's potentially a big problem in production; if a supplier helpfully "fixes" a bug in a board, then the first thing you may know about the bug is when you've tried and tested the product, decided it's OK, then placed a large production order. If that production order doesn't also include the fix, then you're in big trouble, especially as the bug was actully yours to begin with. You just missed an opportunity to discover and fix it inexpensively.
There are two fixes for the problem, neither of which is perfect. One is to put text on each layer of your artwork which says "DO NOT MODIFY ARTWORK IN ANY WAY", or something to that effect, and hope that whoever does the initial processing of your CAD data speaks English and actually cares (neither of which is guaranteed). The other is to use a different supplier, and to let them know upfront that your approval is required for any artwork changes.