Without the access codes, Wesley was not able to disable all the security tracking systems
Wesley asks Robin to access the codes for the security tracking system.
WESLEY: Okay. When you get there, start accessing the codes for the security tracking system. There's something I want to try.
Later on, when being chased, LaForge complains that Wesley has done "something" to the internal security sensors:
LAFORGE: I can't track him, sir. He's done something to the internal security sensors. I'll try bypassing his subcommands. Hold on. I'm picking up a piece of his trail, sir. Sensors show power activation in transporter room three. That would put him somewhere on deck six.
It seems that Wesley did not manage to disable all internal security tracking systems: LaForge can track him via power activation in Transporter Room Three, and Worf can even use thermal sensors:
RIKER: Where the hell is he?
WORF: I am attempting to isolate him with thermal sensors.
RIKER: Narrow the scan field. Go deck by deck if you have to.
A possible explanation is that without Robin's codes, Wesley manages to disable some, but not all security tracking systems. Considering that Wesley had been working on the sensors (albeit not the internal ones) before in the same episode, I think that this is the most likely explanation.