I resigned a player at the end of 2018 season for 3 year. now he appears with 2 year in 2019. I just did the resigning and one year is gone

for confirmation of what i'm saying, check under my transactions

You resigned him with games left in the season so those counted as the first season I think. You have bigger problems, believe me. You don't have an offensive coordinator.

i'm working on it

This is correct, when you sign a player the first year is always the current year. You can also verify this on the contract offer screen, it tells you the actual years in the chart at the bottom.