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You must manually check flagged references under Marked Items.
Currently, Marked Items only apply if a line contains $TEXT ($T). XINDEX records the location of the $T code and prints it out under the "Marked Items" sub-header on the XINDEX report, since XINDEX does not check the references of a $T.
M uses the $TEXT function to retrieve lines from a routine, and routines sometimes incorporate data items that are retrieved in this fashion. Section 2.2.4 of the SAC describes the required format for lines referenced by $TEXT, which states (in part):
2.2.4.1 LABEL+OFFSET references will not be used except for $TEXT references.
2.2.4.2 Lines referenced by $TEXT for use other than to check for the existence of a routine or a line label in that routine must be in the following format: [LABEL-optional]<ls>;;text or M code.
In standard M, a semicolon (;) introduces comments. A double semicolon (;;) indicates that the comment should be preserved even if the routine is compiled. The LABEL+OFFSET syntax is required to prevent errors that could be introduced if lines are inserted ahead of the label. According to the SAC, if code uses $T, the reference must start with a double semicolon (;;).