Without knowing the exact context of all this I would assume there is nothing wrong with your data. Like in many (all?) other fields/analyses, if you use different tools or approaches you will get a different result. However, that does not mean one is more correct than another. Yes, the reads counts themself will differ but it all depends a bit on which “level” you compare the outputs. It is very well possible that in the end, eg. after doing differential gene expression analysis, you will get the same (or roughly the same) list of DEGs. If so then yes, the reads counts differ but the biological end goal remains somewhat consistent.