Subtitles are timed to a framerate (usually 23.976fps or 25fps). The DVD version, Blu-ray version, and streaming versions (Netflix, Hulu, Disney+) all have different intro lengths and commercial break cuts.
"I find it incumbent that you see the inside of a prison cell, Mr. Scofield." How to Use SRT Subtitles Prison Break English Subtitles Season 1 Episode 1