I can think of quite a few ways this can happen. The main variable is to do with the survey performed, so I'm going to talk about that, as this will determine what you want to go for.
So, firstly, planets are very, very big. What you've described as a survey could easily miss even an intelligent race that's not trying to hide. So, you sample the atmosphere, you send probes to certain locations and you have stuff up in orbit. But, did your colonists image the planet?
If the answer is no, then maybe they just sent down landers to certain areas and there was just no life there. Maybe there were only so many landing sites they could be bothered to do. If the aliens are concentrated then you might just miss them (this also works for primitive intelligent aliens, they could be surprisingly hard to to find if they haven't spread to the whole planet yet).
It gets harder for technological life, since the main way we would detect them is by emissions in the atmosphere, or radio leakage. But if there's a small number, their emissions might be undetectable and unremarkable. If they are careful and don't leak radio emissions (say everything is cabled, for security), then they'd be fine. If they had no reason for lighting, they could even live on the surface and you'd never know. I could imagine a technical hive society living that way and there are probably others.
But, let's assume your colonists have actually imaged the planetary surface and taken high resolution pictures. We can do this already to 1m resolution. So any structure would be seen.
But the next question is, what does seen mean? Well, if humans pour all their attention on each individual image, that would be a lot of work. It's more likely they'd get some AI to look through them all and detect "Civilised Structures". But if the alien's definitions are very different to humans, then the AI won't flag them up. Even humans looking at them manually might not know.
Assuming a good optical survey is completed and anything alienish would be detected, what next? Well, maybe the survey focused on habitable areas and not all the planet. But habitable to whom? If the aliens are different and think, say, polar regions are really nice and good for life, but humans are more "let's be near the equator, because the planet is cold and the equator gets close to nice" then we'd just write off an entire area as "not worth survey". It might get cut for funding reasons.
OK, the colonists are anal and have surveyed everything How could the aliens hide?
Well, in one Anne McCaffrey story, humans accidentally colonise a planet belonging to aliens because the aliens came, set things up and, because they had teleporters, went back home for the winter, because winter's cold, man.
On the other hand, maybe the aliens hibernate. Maybe they just went to sleep because the planet has some really harsh variability and it makes sense. Say it gets irradiated every year for a month, and everything that can goes underground or shuts down and is adapted to it (note, you said Red Dwarf, and this actually happens with solar flares, but you may also have to worry about tidal locking with those for your planet). Intelligent life would be in underground shelters having a snooze, or maybe they'd live underground so as not to bother coming up to the surface all the time, or going down. Maybe humans came during a spell when everything looks normal, but life hasn't resumed yet. Maybe the original survery was during a downperiod due to coincidence. Maybe the aliens have woken up and gone "OMG there's an alien spaceship orbiting us, let's not go topside just yet!" and have the structure to hold out a bit because they're adapted to do that for one or two periods in an alien year.
In the tidal locking scenario (where the planet stops rotating because it's close to the Red Dwarf) maybe the aliens live on the night-side, where it's permanently night, for reasons. Maybe they evolved that way.