Quite simple - for example soil condition can be very badly suited for species what humans grow. Or ecosystem can be extremely hostile for such species. Many reasons.
1) The planet's native life all evolved with left hand DNA.
2) The terraforming technology did it's best, but the native plantlife remains toxic to humans.
3) Changing the temperature and atmosphere so much caused microbial seeding to go nuts and the microbes killed off all large scale plants. Only algae survives, and the animals willing to eat it.
4) What happened to the Vikings in Iceland (read
Guns, Germs and Steel). TLDR, the food was there, they just didn't use any of it because of weird cultural phobias. So you terraformed a planet and now it is chock full of fifty pound, ten foot long, highly nutritious edible earthworms. Yummy! Wait, where are you going?
5) Oh crap, we forgot to add wolves! Rabbit swarms devour everything as soon as it sprout.
6) Plant life grows great here, especially the native
Triffids.
Etc...