Are you referring to a script in screenplay format or a transcript? In both cases, formatting and elements you don't want indexed need to be considered.
In screenplay formats, you need to ensure that only the dialog is being indexed and not all the other Action, Scene Heading, etc. This is done by ensuring that all dialog starts "n" number of spaces of left margin. Screenplay application like Final Draft do this as a matter of course and all you need to do is "save as text with layout" to preserve the look. In the script settings, you can select "dialog" from the script and it will do the offset identification for you.
Less formatting that a screenplay, but still some considerations as to items you do not want indexed and synced. For example, for an interview type transcript if the interviewer and interviewee are labelled, then you want to make sure there are [ ] around that. The brackets tell the indexing engine to ignore what's in between. Same for timecode, and anything else that would not be part of the dialog being spoken in the footage.
Also, for long transcripts, you will want to have more granularity since the indexing is line based. You can make the amount of characters per line shorter by setting the margins larger before saving as text with layout.