1. If passport was to expire within 6 months, custom and border immigration officer (BICE/CBP) made the right decision. And you can only regain new I-94 by filing with USCIS, re-entered US, or if lucky, get it in local CIS office.
2. If your passport still will be valid for at least one year, you don't need to renew passport now. If expiring within 6 months, you must renew it before filing for a new I-94.
3. It's at local CIS office's discretion to correct or not correct the I-94 date, because they are the USCIS people, may not want to take responsibility of the act that done by BICE/CBP people (USCIS and BICE used to be together known as INS, but INS split in 2002) So local officers may ask you to file with USCIS service center even it's not your fault, so ask local office about their policy first.