Why was the number of MiG fighters not obvious earlier on?

The idea in the movie is that the enemy fighters were flying so close together that what should have been five radar blips looked like only two. I don’t know at this time how likely that is to happen in real life, but it is certainly plausible.

Radar is not a magic viewing machine. It’s just a series of radio waves sent out in front of the plane that hopefully bounce off of anything out there and then are picked up by an antenna, also mounted at the front of the plane. On a fighter jet, the radar transmitter and receiver are hidden inside the nosecone.

Radar just tells you something is out there. It doesn’t tell you what it is. Radar is designed to only show a blip if it’s a chunk of metal the size of an airplane, but sometimes a flock of birds or other things can show as a contact. As you get more bounces back, you can also learn how fast the thing is moving and in which direction. The more often you bounce a radio pulse off of the unknown contact, the more you know about it. But since the contact can detect your pulses and determine where they are from and what frequency they are, focusing your radar on a contact can often tell the contact more about you than you can learn about the contact.

Furthermore, it's not even possible to tell that the contacts are MIGs at all with radar. Based on speed and changes of direction, it's reasonable to conclude that some contacts are fighter jets rather than other types of aircraft. Also, military craft carry special transponders (called "IFF" for "identify friend or foe") that are supposed to respond when queried with a signal that indicates whether the aircraft is a friendly or not, but mainly that only would tell you whether another craft is a US military craft, not necessarily whether it's an innocent civilian plane or even an allied aircraft. And radar does not have the resolution to show the outline of a contact. To find out what kind of craft it is, you have to get close enough to actually see it. In the 1980s, when Top Gun is set, there were actual BVR (beyond visual range) kills of Libyan fighters over the Mediterranean, so waiting for visual contact is a very tense thing - you can be shot down by aircraft before you even know what those aircraft are. They only waited in Top Gun because they were not authorized to fire on unknown contacts and they did not have the AWACS available to tell them more about the contact.

In commercial controlled airspace, aircraft are required to have radio transponders and to identify themselves frequently. In international conflict airspace, it's more like hide and seek.

So it is plausible that the MIGs depicted specifically used a tactic of flying dangerously close together to hide their numbers, and also had their own radar turned off so that they would know more about the Navy F-14s than the Navy pilots knew about them.

Note that the carrier radar is much farther away and tactically would want to scan the entire area rather than focus too much on any specific contacts. And there is no such thing as satellite radar. The only detailed information the fighter pilots have is from their on-board radars. It is theoretically possible to have high-flying radar craft (AWACS) to have more information about what is going on, but in international airspace it could be that deploying those aircraft would escalate tensions.

You may find this edifying:

https://gizmodo.com/how-fighter-jets-lock-on-and-how-the-targets-know-1644871272