My puppy's internal suture knot cut off by vet..

My puppy was spayed by the rescue's clinic about 1 month ago on 4-14 before she was sent over from SC. She is estimated to be about 14 weeks now as we don't actually know her birthday. I got her on 4-30 and all her stitches were dissolved except for the internal suture knot. This started to cause her irritation last week and she started licking it. She got a pimple like bump next to it. No puss, didn't look angry or red. Just a white type of bump there. I tried warm compresses with no change. The vet saw it today and cut the knot off completely. There is nothing on the outside of the skin anymore. The lady from the rescue said this can cause the internal stitches to unravel and it should take a while but be allowed to dissolve on its own. So what do you know about this? Should we have left it? Was it too soon or will it be ok? Is the internal stitches ok as long as the external have dissolved. I'm just worried.

Thanks.