In the early stages it's sometimes difficult to count, especially rests and longer notes. Something needs to be there at the point where you don't actually play a note - either because the last note lasts longer, or there's a rest.
Various things can help, whether it's a nod of the head, shrug of the shoulders, tap of the foot, or even a sniff. In other words something that you do to fill the gap where there's no note to play.
Another way, which worked for me, was to count either as you try - 1e&a2e&a, or use numbers 1-16. Count out loud, and use single syllables - 'sen' for seven, 'fif' for fifteen, etc., and shout out the 'unused' ones, signifying the lack of note being played. As usual, slow it all down initially.
If you are reading music, and playing scales, an interesting thing to do is write out some bars using the dots, in different rhythms, and play your scales in the timing you've written. It may help, for example, with a two octave pentatonic scale, to have 21 playable note places, but of differing lengths (not all of them, obviously!).