Around 5 weeks ago I had my hall, lounge and dining room fitted with american black walnut and now I can see that where the knots in the wood are some of them have been filled with a type of filler. When I purchased the floor I was assured that it was part of the wood and should have no problems with it. Five weeks later and this filler has started to break down and come out leaving holes in the floor. At the moment the largest hole is about 5mm by 3mm but some knots have be filled that are an inch round and you can see it starting to break down around the edges. Is this a common problem with filled knots and is there anything that I can do about it?

Any help will be greatly appreciated.

North American Black Walnut commonly has knots, especially in wider plank solid floors. Any filler/putty used in the knot holes should be permanent and you should not be having problems with the filler/putty/patch coming out. I would promptly call the seller and notify him/her of the problem. And I would encourage you not to do anything to the filled knots at this time. It is the seller's/contractor's problem and they are the ones to rectify it.