No, it doesn't! This is the habitual hu- tense (which you may not have learned yet: it comes later in the course). To give an example in context: Kwa kawaida Rashid hukimbia kila siku, 'Usually Rashid runs every day'.
In the negative tense, the final '-a' changes into an -i (1). E.g. Hukimbii meaning 'YOU are not running'. And so 'he is not running' would be
(1) but only in the present tense
'He is not running' would be 'Hakimbii'. 'Yeye hukimbia' means that he/she runs regularly, it is the habitual tense(you havent been taught this yet). It would be 'hakimbii' because 'Ha' - negative prefix for he/she, the tense marker disapears in the negative present tense and 'kimbia' turns into 'kimbii' in the negative present. I hope ive explained it well.