Makoto wastes her last jump during the phone call with Chiaki. Then comes the big bike crash. Chiaki jumps back in time and prevents the crash, using his last jump in the process. Makoto later realizes that Chiaki's backward jump undid her last jump, so now her arm reads "01" instead of "00". But wait...if Chiaki jumped back and undid Makoto's last jump, then she's never experienced that jump, because retroactively it never happened. (Similarly, she doesn't remember the aftermath of the bike crash.) So why is she surprised to find "01" on her arm? From her (new) perspective, it never said "00" to begin with!
Makoto seems to remember more than she should after Chiaki's jump, for reasons that are not really clear. She shouldn't remember seeing Kousuke and Kaho go by on her bike, either, but judging by her conversation with Chiaki she does remember that part, even though she doesn't remember the aftermath he describes to her. Possibly it has to do with the time freeze that he instigates in order to get the chance to explain to her, rather than the simple reset that every other time leap in the movie causes.