Some of these are notated in ways that are a bit confusing (though the alternative might be a bit confusing too, for a percussion instrument). Looking at m. 50 and those like it, the first quarter note occupies all of "beat 1." But the eight rest that follows "pushes" the subsequent quarter notes, so that they both occupy the last half of one beat and the first half of another. These kinds of rhythms are often printed, instead, in ways that break these quarters into tied eighths so that the beats can be more clearly seen:
Of course, on an instrument like the shaker that has no sustain, I suppose this might confuse some and they might think they should play on each eighth note.
It might help you, as long as you understand what you're doing, to write out some of the measures this way. For instance, m. 25 becomes:
After that it's just a matter of understanding how the out-loud counting "1 & 2 &" aligns with the actual quarters and eighths.