Okay, so I'm trying to stick to a routine, both eating and exercise but inevitably I do have days like today.
I ate a whole grain english muffin with peanut butter for breakfast at 6 am (I'm usually not all that hungry in the morning) then I went to work, was in surgery all morning, had time for a handful of baby carrots while I cleaned up the OR then went right into a bone scan where I spent the rest of the day, then at about 5:30 pm I finally had time to eat my lean cuisine meal (again, while I was cleaning up after the scan) and that's it. So I've eaten hardly anything (but I'm not hungry because my lean cuisine came around dinner time) only around 650 calories and I'm too exhausted to work out because I spent 12 hours on my feet (plus I'm not sure if I should try to work out on a day where I've taken in so little fuel).
I'm worried that this is really bad for my body, however in this case it was just one of those days where I didn't have the opportunity to eat every 3 hours like I usually do and there's really nothing I could do about it. Does this screw up my metabolism? Will this cause me to stall? These days come along atleast once every couple of weeks, sometimes once a week...is there something I can do to counteract them?

I'm with the others who say that better planning would help. Clearly you can't control your work environment--but you can make sure you have better foods available for those days when breaks are hard to come by. Snacks like Kashi bars, FruitFast bars, and other healthy food bars come in handy, and they keep indefinitely if the wrapper is unopened. Other ideas: slice up an apple and put it in a zipper bag. (If it goes a little brown, that's OK--or you can put some lemon juice on the slices to prevent that.) Peel an orange and put the segments in a zipper bag. Hard boiled eggs also come in handy, and they keep for a day or so in the shell without refrigeration. 