New bathroom fixture won't fit

I am trying to change out the faucet fixtures in my bathroom - 30 year old house. When I removed the old fixture it was attached to the water supply with copper tubing. When I tried to put the new one on, the pipes did not line up 'exactly' with the drilled holes. It is off by just enough to not fit! Any ideas? I got the standard 4" faucet fixture, do they come in different sizes? I guess since the old one had the flexible copper tubing, the hole placement was not as critical. Thanks!