If someone can make time dilate, this must done in a way that this ability useful. It shall be assumed in this answer this time dilation power only works on people and things in the immediate vicinity of the character with the power. If her power encompassed the entire planet earth nobody would notice anything had changed with the possible exception of astronauts returning from deep space.
But let's start with the not so useful version of her time dilation power.
If, in contrariwise case, she made time in her vicinity and if this includes herself, then while she and people nearby wouldn't be aware their time was dilated, i.e., moving more slowly than for people and things outside her field of influence.
The shadow organization might her doing this by observing one of their nefarious operations going wrong by her accidentally dilating time. If this happened several times and she was always present this fact would enable them to discover her and her powers.
She could employed to slow down time in specific areas while the shadow organization does its nefarious deeds.
But that was the not so useful case. Now for the more useful case. This time her time dilation power slows down time people and things in her vicinity but she remains unaffected and moving her normal rate of speed. Any shadow organization that accidentally crossed her path while she was in time dilation mode would observe everything around he was time dilated but she was still moving normally. Your average criminal mastermind should have no difficulty deducing what was going on, and put her on their payroll or coerce her into using her power for evilness.
This answer has sketched two possible modes by which a time dilation power might work and its affects. Like ChrisM, she could be detected by the affects of her time dilation. The likelihood of her detection will be increased if the character and the shadow organization cross each other's paths.