I noticed this happening twice already, the first time i noticed it i used version Krastorio 0.9.9 & Factorio 0.18.15. The 2nd time i noticed it I was using version 0.9.14 & factorio 0.18.21 , but both bases where pretty near each other and I dont really know if the road was there all the time and I just didnt notice it.
Little detail i just remembered (was a few weeks ago so im not sure how accurate it really is) , i was building the road first and removed the creep later, and suddenly there was road under the creep where at first i didnt even build it. But the 2nd time (the one i reported) I found it under creep they were like 10-20 blocks appart.
Hopefully that helps.