Bundler installs sqlite3 every time, but there's not sqlite in Gemfile
(Even though you've figured it out, i'll put it here incase for some reason people don't read the comments)
The 'taps' gem (http://rubygems.org/gems/taps) that you've required in your Gemfile has a runtine dependancy on the 'sqlite3-ruby' gem.
You can ususally find out where strange dependencies come from by looking in your Gemfile.lock file, as you can see here...
taps (0.3.23) rack (>= 1.0.1) rest-client (< 1.7.0, >= 1.4.0) sequel (~> 3.20.0) sinatra (~> 1.0.0) sqlite3-ruby (~> 1.2)Each gem will be listed with its runtime dependencies along with the version that it needs.