These two boxes describe two overlapping but different things.
The code W amount on box 12 on your W-2 includes what your employer contributed in 2018 PLUS what you contributed through payroll deduction in 2018.
Box 2 on the 5498-SA is
1. the sum of all contributions made in 2018 (both Code W and direct contributions)
2. any contributions that you made in 2018 for 2017
3. also includes any trustee to trustee transfers from an IRA to the HSA.
4. however, any excess contributions for 2018 are not included in Box 2.