The whole foot positioning thing is such a pain for FED this year - we got a 45+ minute dissertation at our Spring interpretation meeting and then some did their own thing anyway. I even saw "veterans" who were part of the presentation not calling it. They also avoided the other POE - the swinging free arm with a ball in it (some call it the ape arm others call it the elephant trunk arm). There were some that felt in the stretch/set the free foot had to be within the bounds of either edge of the rubber (think drawing a line from the short sides of the rubber straight down the mound - eg a 24" wide area) - that may have been true at some point in time or a misinterpretation of the foot entirely against the rubber.
Anyway, in FED it essentially states for a full wind up - pivot foot must be in contact with rubber and non pivot foot "on or behind a line extending through the front of the rubber". From the full windup - you have a choice to step off properly using pivot foot first and breaking your hands or throw to the plate. For the stretch/set, the pivot foot must be "entirely in contact with or directly in front of and parallel the pitching plate". Basically touching from heel to toe (or toe to heel) the rubber. The free foot has to be "in front of the line extending through the front edge of the rubber". From the set, you can disengage properly, throw to a base, or pitch to the batter.
So if a pitcher has his free foot in front of the line extending through the front edge of the rubber, but the pivot foot not completely in contact (eg, the alleged "hybrid" stance), then it's a balk for FED. Typically this is a case where the feet are angled. I've seen pitchers later in the year work around this by standing at the angle, but with the ball of their pivot foot on the rubber and their free foot heel right on that so called line. Still looks hybrid, but within the rules. Again, they can only step off or pitch - so there's no advantage here. Wait for first movement of non pivot foot and go if you're the runner. React to the step off.
So back to the OP - probably not a balk - unless of course it was felt the entire pivot foot wasn't touching the rubber or it was felt the free foot wasn't in front of the rubber (either is tough to tell from 60' 6", but not impossible). While you cannot argue a balk, you can ask politely what was done wrong. Then whether you feel it's right or wrong - it's probably going to be a balk for the rest of the day/game - so deal with it. Doubtful you'll get a change of opinion on the field.... Although I suppose it's a rule interpretation and that is protest-able right? As long as you understand the reason for the calling of the balk over foot position.