-Yes, there is a big problem and it will affect your I-485 also. When your I-94 expired, your H1 status is invalid even if your H approval notice I-94 is still valid because your lastest I-94 (the one you entered US with H1 visa) has overwritten the H1 approval notice I-94. I suggest you not to go outside U.S. now and have to go to CBP to see they can fix it for you or not.
There were a few people who had the same problem as yours in this forum.
See: 置顶: 经验之谈:入境时,I-94被愚蠢的海关官员弄错了怎么办?