Sadly as there is no further explanation on why Qui-Gon called Maul an it we can only take a guess. A very educated guess though.
We need to take into consideration that the fight lasted only mere moments and that the star warsStar Wars universe contains A LOT of different species (even two legged ones). With some of the species looking very similar to each other and also some having 2 genders, some 1 and some probably more than 2.
As a Jedi, Qui-Gon travelled the galaxy a bit but probably has probably not seen every species already, yet. Thus the information above combined with the shortness of the battle, it is very probable that Qui-Gon was unable to be completely sure what species Maul hailed from....and also what gender he had.
Thus calling Maul an it is the most neutral method of talking about Maul (I dare say even the Jedi way it is that way......as it is th emost evened outthe most even way of talking about Maul without implying something that the Jedi was not sure about).