The situation is quite simple: You cast detect thoughts, and you have two targets within your cone that both fail their will saves. Does the caster immediately know which thought belongs to which target? I haven't been able to figure it out from the spell description, is there even a RAW interpretation for this?
It doesn't say
It could clearly spell it out, and it doesn't.
But there are clues
First, the spell says the amount of information revealed depends on how long you study a particular area or subject. This spell requires concentration.
Second, the rules for the second round say you learn information about each creature in the area. They then elaborate if you attempt to read the mind of a creature of INT 26 or higher whose score also beats yours by 10 or more, the spell immediately ends and you are stunned.
Combined these imply you can focus on an individual or individuals within the area of effect, or probe the area generically. It doesn't say this, but it is the most reasonable interpretation.
You learn specific information about each affected creature - that it is conscious, has an INT >= 1, and is thinking at the moment.
Finally, the spell says the results depend on how long you study "a subject" and say you can detect the surface thoughts of "any" mind in the area, not "all".
This implies the ability to pick and choose which minds you want to detect surface thoughts from. It doesn't make much sense to then say 'but if you target more than one, you can't tell which is which'.