Rightly or wrongly, mortgage lenders typically view risking to the self-employed as riskier than lending to employees, especially where there are irregular or complex incomes involved.
Employees normally have a set income that is paid on the same day each month, and this regularity, perhaps unsurprisingly, puts lenders at ease. Where you're self-employed and have an income that varies month by month, lenders will typically be more cautious.
There have been frequent calls on behalf of the self-employed, sometimes from brokers themselves, for lenders to make the process of obtaining a mortgage easier. Whether or not this ultimately happens, you should do what you can to ensure your application has the best chance of succeeding: save up a decent deposit, spend time getting your credit report in order, and gather all the relevant proof you need to prove your income.