Whtat phospholipid composition do you use ? And at what temperature you conduct hydration? 

After hydration you could sonicate liposomes from around 10 minutes and then extruded through 100-200 mm filter. You must have SUV  liposomes. Another thing is after hydration it was suggested that around 5-10 cycles of freezing and thawing of the liposomes could improve and shrink the space between the phospholipid layers. 

If your liposomes are composed of two different lipids or more, check the transition temperature of each lipid and make sure your liposomes are not disrupted or damaged during the hydration process. Sometimes multilammelar vesicles are formed due to a very high concentration of your lipids also. I suggest to try to measure with dynamic light scattering also (DLS) 

Following hydration, you can control the size of your liposomes with sonication. Depending on the tip sonicator available at your lab, you can optimize the sonication time with on/off cycles. For DOTAP DOPE liposomes for instance, with amplitude 10%, pulse on 10 sec, pulse off 15 sec for 1 minute I get SUV , with an average diameter around 100 nm. 

If sonication is not an option, due to availability of a probe sonicator or incompatibility with your formulation, you may want to try some freeze/thaw cycles before extrusion. The other parameter you want to keep under control is the temperature at which you are performing the extrusion process. Try to keep it at 5-10 degrees higher than the one of the lipid with the highest transition temperature. I have seen myself that working close to the transition temperature may give some unexpected behaviours, like multilayering and instant caking of the vesicles.

I agree with Marco's comment about performing the extrusion above the phase transition temperature of the lipids. I'd also ask what pore size are you using for extrusion? A pore size of ~100 nm will reliably produce unilamellar liposomes. Larger pore sizes will not.