So many things here but let me start. Many of us store eggs for incubation like that and have pretty good hatch rates. How long did you store them like that? If it was less than a week you should have developing chicks.
It’s not at all strange with that thermometer. They are tremendously unreliable. You say you trust that thermometer. I hope you have a good reason to actually trust it. I don’t trust any until I can check them out, usually using a liquid-filled medical thermometer I do trust to check them.
Do you have a still air or forced air thermometer. That’s a little high for a forced air, those should be closer to 99.5 Fahrenheit. Inside a still air, hot air rises. It’s extremely important where you take the temperature. It yours is still air and you are taking the temperature at the top of the eggs, that’s pretty good. If you are taking it somewhere else, that’s not good.
Some people can see inside eggs really well and may be able to see development after three days of incubation. The color of the egg shells, the equipment and technique you are using, and your experience all factor in. I don’t bother trying to candle my eggs until Day 7. Even then I can’t see anything in a lot of the darker green ones. I certainly would not do anything dramatic until a lot later. Normally I toss the clear ones when I candle at day 18, going into lockdown, not before.
How are you counting the days? A whole lot of people get this wrong. An egg does not have a day’s worth of development when you put it into the incubator. It takes 24 hours of incubation before you have a day’s worth of development. Say “1” the day after you start. A good way to check is that you should say “21” the same day of the week you set the eggs. If you started them on a Tuesday, Day 21 will be on a Tuesday.
You are setting pullet eggs. I do too, you can get them to hatch. But pullets are famous for laying strange eggs when they first start to lay. You might get soft or no-shelled eggs, extremely hard shells, double yolked eggs, no yolks, no whites, or just plain weird eggs. It sometimes takes them a while to get the kinks out of their internal egg making factory. These things plus a lot more need to be right for an egg to develop and hatch. A lot of them get it right from the start, but I normally don’t get really great hatch rates with pullet eggs. Sometimes things that you cannot see just aren’t right. The longer you can wait to set them, the better your chances.
Another problem with pullet eggs is that they are small. There are just not enough nutrients or room in there for the chicks to develop into big strong chicks. Most of the ones I hatch from pullet eggs live, but the mortality rate for chicks from pullet eggs is higher than from eggs from older hens, even a month older really helps this.
Right now I would not panic. Don’t do anything dramatic or drastic you might later regret. Wait a few days to candle again. Be patient and treat this as a learning experience. You still have a chance to get chicks out of this.