Usually I only get the nozzle hitting the layer below when there are overhangs and only in those regions. There is a lot of discussion. There are a few possible fixes - the most common and most successful is more fan. But I suggest you read over some of this:
http://umforum.ultimaker.com/index.php?/topic/4094-raised-edges/
Look at the first picture in the first post to see if this is the same problem you have. Then skip right to "page 2" and look at foehnstrum's video and read all the posts after that possibly. It's not until around post #39 and later that we really begin to understand what causes the issue. That video was important and looking with "reading" glasses.
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IRobertI 521
Sounds like pillowing to me, which is a bit more likely to happen with very thin layers. See more info here:
http://support.3dverkstan.se/article/23-a-visual-ultimaker-troubleshooting-guide#pillowing
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