I think they made a mistake by not considering the size of the balloons. There is huge difference between the large spy balloon and this small balloon. The payload of the former was bigger than envelop of latter. They should have been able to tell from the radar but definitely from the fighter. Most concerning is that nobody thought about it and the response seems to have been panicked.

I think these are 'better safe than sorry' cases, and that as more data rolls in they will re-calibrate. Look at it in an adversarial way: whoever wants to spy on the US could easily try to make the gear small enough that it would be taken for something innocent, and then to use a satellite uplink to move the payload off to the mothership. The question isn't really whether or not this particular balloon was a mistake or not. The question is what the minimum size is of a balloon that is still a viable spying platform. I don't have the answer to that question, but I've seen some pretty impressive miniaturized gear that I think you could easily take up with a small balloon, enough to be worried about it from a counter espionage point of view.

What evidence do you have that nobody thought about the size of the balloons? That's a comically unlikely take.

The fighter can only slow down to like 180 knots, while the balloon might be blowing around at 10-90 knots depending on where exactly it is. How close do you have to be with the Mark 1 eyeball to actually disambiguate this kind of target, how long would you actually be at that range in a fly-by, and how many fly-bys are you willing to do before "whatever, we will just apologize to the NOAA or a college somewhere" and shoot it down.

Maybe the targeting pod could give you a zoomed up view, but it's not really designed for nearly stationary, high altitude objects.