I obtained less than 0.5 ng/ul of capture libraries while the amount of individual libraries were as expected; what are the possible issues? 

Usually with most of our panels the amount of DNA we quantify after the capture is between 10 and 30 ng/µl. Low yields may be related to several problems:

• incomplete denaturation step 
• a decrease of temperature after denaturation and prior to the addition of the probes
• omission of probe addition
• Loss of material during the wash steps (?)
• Problems with post-capture amplification
• Loss of material during cleanup