Sure there is.
Puppet will attempt to install / update packages if it doesn't think the ones currently installed satisfy the relevant Package declarations. Note that it will always check all declared Package resources -- don't confuse that with trying to install or update packages. There are not many config files you could change that would alter Puppet's opinion about whether Packages are in sync with your declarations, but there are a few.
Starting / restarting services is rather more likely, as denmat said. If you have declared that a given Service should be running, then Puppet will attempt to ensure that it is running, every time the agent runs. Moreover, if you have made a Service subscribe to changes to its config file (or any other file), or set up the config file to notify the service of changes, then Puppet will restart the service each time it changes the file while the service is running.
A key question here is whether Puppet attempts to install / update packages or (re)start services if you run it when not expecting any changes. You perform such runs all the time if you run the agent on a fixed schedule, but you might not do if you run it only when you think you have changes to apply. In other words, you should verify that the unexpected behavior is actually correlated to config file changes, and not a routine outcome of your manifests. The likely causes of the problem are quite different in one case than in the other.
John