Would +.010/+.000 be violated by a +.001 deviation?
Would +.010/-.000 be violated by a +.001 deviation?
For certain, by what you have written so far:
+.000/-.010 is not violated by a -.001 deviation, but
-.000/-.010 is violated by a -.001 deviation.
The problem you had should have had speculation stop immediately at a call to the responsible engineer and whoever from manufacturing and QA/QC signed the drawing as ready for production. No need to guess about the signs or anything else.
Of course, this would not detect other interpretation errors, but having engineering review and sign off production and QA/QC plans would close the loop as much as possible and there would be no need for a call for this case at all. I doubt many companies do this, mostly because the cost of defective interpretation is preferably a hidden cost that comes in when schedules are delayed when manufacturing/QA/QC delivers unusable product with an argument about drawing deficiencies.
As a side note, it used to be that manufacturing wanted the first tolerance to be the first limit hit; in boring a hole the -.003 tolerance would be place above the -.000 tolerance. That way missing the tolerance would leave more material and an acceptable part. If they over-bored the -.000 tolerance, they would have a scrap part. The opposite was true on external features.