This is not true. There are many people that saw Hannah;she was with a number of people, though maybe briefly that night. LE has information that JM was together with Hannah that night and my guess is that the bartender, other staff, or other people did id JM and Hannah leaving Tempo's that night at a certain time when she disappeared and there is no further video footage or sighting of her after that time.
For some other reason, the car was targeted as suspicious. You don't get warrents to search the car of someone for just the above reason. Plus they cannot tie him to his own car. So they got the warrent to search the car, enough evidence from that search to seize it and also something in that car that was sufficient to get a warrent for an apartment search, but still not enough to charge JM.
My question is how did the car get involved in this? What did LE have in terms of info to get that car searched, seized and apt searched? Would the fact that JM was the last person that LE could track to Hannah be enough to get his car searched? Did he agree to get his car searched and then they found something in there? A lot we don't know.