You've probably broken one of their rules, or wronged one of their beneficiaries. For example, one rule of the Thieve's Guild is to avoid killing at all costs. If you were reckless, and killed a lot of people while on a quest for the guild, they may see you as a traitor, or someone out to give them a bad name. Alternatively, you can be kicked out of the guild for stealing from the Black-Briar family who supports the guild.
There should be an option for you to pay 1,000 gold in reparations to be allowed to enter the guild again.