Toe overlap on mountain bike
It is known some people moving to 29er's have issues with tow overlap, especially on small frames. I know when I am not using cleats, I sometimes get a bit of toe strike, less so now, but initially it was happening regularly.  

Best not to try and 'fix' the overlap - the bike geometry will be negatively affected unless extreme care is taken. Its not a major issue, you get used to having to keep your feet back (where they should be for efficient riding) Clip less pedals solve the problem completely.  

There is a reason the industry quickly moved to 650b. One take is one size does not fit all as the failed 29 experiment shows. The other (cynical one) is the industry needed a reason to sell more bikes, so they came up with 29er as the new "must have" for a couple of seasons then introduced the 650b and said "this one is much better again", knowing all along 650b was a better "one size for all" size.....