I was reading a post from Gerry Miller about how he was statting writing up the Solomani Rim and using UWPs from the classic supplement. One problem was a slew of Garden World that were also Barren (no people, no boats, no planes no motorcars.) To me this is no problem. The UWP is a starting point for a planet. There is a lot it doesn't cover and if that isn't by design it should have been.
An otherwise lovely planet might have atmospheric taint. Taint can cover a lot, from chemical, biological or radiological contamination. A nuked planet might have plenty of prime real estate but moving in is not advised unless you want to glow in the dark. Similarly, super viruses and bacteria might taint the air, incurable, fatal, and contagious.
A planet without a taint may still have an ecosystem that's hell on grav modules. Our world has plenty of examples of hard to kill off venomous pests (we keep them in a place called Australia.) True your bear and lion analogues will fall prey to the intrepid Scout with the laser rifle. But what about fly analogues, say, bearing disease? You may not always have a flyswatter nearby and what is the required Dex for it? Of course you could fill the air with insecticide but then you might wind up with a tainted atmosphere, brining us back to step one.
Lions and bears are bad enough but a world where the predators use psionic assault really opens up new vistas of terror.
Aside from the autotrophs and heterotrophs a planet's place in the planetary system may not be ideal. Red dwarfs may account for a number of habitable worlds. But that doesn't mean you'd want to live there. Most likely such stars will have a garden planet orbiting close. Aside from having air you can breathe such a planet will not have a lot going for it. It will probably be tidally locked restricting usable land to a thin belt between the day and night sides. You'll have gloomy skies, nearly constant winds and storms as air circulates between the light and dark sides. You primary might also be old and crotchety and show you the love with frequent bursts of radiation and EMPs.
On more Earthlike worlds you may just be looking at planets that are too hot or cold to be comfortable or habitable. Though excessive ultraviolet and solar storms are still possibilities. Atmospheric storms are no joke either. Your planet may even be going through a massive climate change. Prehistoric humans were nearly wiped out by one such upheaval.
Let's talk tectonics! Is your planet stable? Excessive earthquakes or volcanoes popping may make your would be settlers bail for an L-5 colony. Just add an oversized moon or have the planet orbit a gas giant. Besides earthquakes you could look at floods. Add a high oxygen content to a planet and you could have fires as well.
Hydrographics are a tricky subject. Ice caps are considered part of hydrographics (this is how an airless rock can have a hydrographic rating.) Maybe that 80% water covered planet actually is covered with glaciers a mile thick? What if most of the land on a world is marsh and swamp with no solid ground for buildings?
A planet may be inhabited but rated Barren. Perhaps it contains a population of semi-sentients that aren't considered sophonts just yet? A Scout base might be a good indication of such a population. The Scouts are observing them cautiously from an orbital station. Colonization is prohibited.
Ancient artifacts and bases will also lead to a planet being taken off the real estate listings. While some situations will warrant a full interdiction some will be hushed up and other reasons manufactured to delay colonization to keep such bases a secret. An interdiction zone is fine if you have the ships to back it up. A government with few ships or surrounded by more powerful neighbors will go for secrecy.
A mundane reason for listing a planet as Barren is a transient population, one without industry to support itself and no formal government. A planet given over to quarantine medical patients, a nature preserve for vacationers, a research facility or a holding area for prisoners are possibilities.