Establish that the 'missing' APs actually work by unplugging a known-to-work AP and plugging the missing ones in. Check they power up, talk to WLC, etc...
If they register successfully, then it's likely a switchport config / cabling issue. If your failing APs are all in specifc areas / grouped together, it could also be worth considering other things like there being something wrong with a whole VLAN, Switch, etc..
If APs don't register, then could be a number of things;
1. AP is actually running IOS(!!)
2. AP has an SSC instead of a MIC, and the SSC Hash / AP MAC isn't installed on the WLC
3. AP has an inappropriate Static Config
4. Broken AP
Solutions
1 - Migrate from IOS to LWAPP using LWAPP Migration Utility
2 - Add the MAC & SSC Hash to each WLC in your mobility group
3 - Factory reset the AP to delete the static config
4 - RMA!