My explanation above is not correct (I will flag it after posting this). @lauren.j.mciver pointed out that your MetaPhlAn profile has extra output columns from running in a non-default mode. This is the source of the error (not the added read count). We discussed this recently here as well:
If the alternate MetaPhlAn output is becoming more popular with users we can add some robustness to the extra columns in a future HUMAnN release. Sorry for any confusion caused by my earlier reply!