Deseq2 Error: Differnt number of rows in featureCount files

So, I had two datasets A and B, and featureCount files for each. When I use these files as input in deseq2, it gives me the error:
Error in data.frame(…, check.names = FALSE) :
arguments imply differing number of rows: 4659, 4644
Calls: get_deseq_dataset … eval -> eval -> eval -> cbind -> cbind -> data.frame

I understand that the total number of rows in each featureCount file is different, how do I overcome this?