The numbers (as in one, two, three..) are actually generally from Chinese, with exceptions (particularly where there are two options, as for four and seven), but counters (for smaller values) are generally from native Japanese and therefore sound different from numbers, and also changes somewhat with whatever it is you're counting. Japanese is so logical and well-structured that it appears that to compensate for that ease, you have counters.. (though we could blame Chinese for that as well, pre-contact there were only a very limited number of counter types (counter types are flat items, round items, long thin items, people, years..), post-contact there are hundreds (but fortunately it's possible to ignore a lot of them).