That's most likely it. I've built just enough cross-training durability to be able to do pretty respectable 5k/10k runs routinely, but not enough volume for my body to really adapt to the stress.
So probably each week when the runs get inserted, the body is like "wtf you doing to me, mate?" Even though the runs "feel good" as in no pain at all and you feel you can give it some gas if you want to.
I'm doing this to myself because they haven't posted or permitted the local TT series and if they don't soon I'll sign up for a local duathlon instead in April. TT regionals is around same time in May as last year. For that I'll cut the run volume out after the duathlon and only do TT work.