Homemade cheese sauce made without processed cheese usually has a slight texture to it. However, it shouldn't separate and be clumpy. If the cheese sauce has separated, it is likely that the stove heat was too high. It may be curdled. Immediately take the sauce off the heat, and add a splash of cold milk to lower the temperature. Whisk quickly. If that doesn't work, you can try adding a tablespoon of flour and whisk that in quickly. If neither of those things work, the sauce may be beyond repair. To save it, you could strain it through a sieve to get out any clumps. If you have any tips on fixing broken cheese sauce, let us know in the comments below.