The VF-25 probably does have wing hard points but, I haven't seen any literature on it. Maybe in the Chronicle or in a later DVD liner notes. In episode 17, we see Alto's, Michel's and Luca's VFs carrying reaction missiles. So it has something.
At this point, I'm gonna say that the missiles we saw in episode 1 were an animation mistake. Both DVD/Blu-ray editions and TV airings never fixed it. So it's either an animation mistake or perhaps there was something off-screen firing missiles at the red guy and Gilliam's VF-25 happen to be in the same direction.
Internal hardpoints? I'm looking at the model and I don't honestly see how one could even fit a mini-missile launcher around there.