Batch effect present for some biotypes after running CombatSeq

[kvn95ss]

I'm working with smallRNA data and performed batch control with Combat_Seq (bioconductor version).

I used the below command -

library('sva')
corrected_batch <- ComBat_seq(as.matrix(counts), batch = coldata$Small_Seq_Batch)
corrected_batch <- as.data.frame(corrected_batch)

Here's a MDS plot before correcting -

And here's the after

What could cause this? I tried separating the biotypes first then performing the batch correction, but the outcome was pretty much the same.