if you mean you want to insert the string:
INSERT INTO MyTable (MyColumn) VALUES ('([phonenumber] like '%%')')
Then it's not the percent sign that causes the problem - it's the quote characters.
INSERT INTO MyTable (MyColumn) VALUES ('([phonenumber] like ''%%'')')
Will fix that.
If you means that you want phone numbers that start and end with a percent character then try:
SELECT * FROM MyTable WHERE phonenumber LIKE '[%]%[%]'
If that isn't what you want either, then we need much better information.