6G networks require precise and secure clock synchronization for the success of promised applications. The growing demand for high accuracy and precision in clock synchronization motivated the development of QTS protocol. The security of the QTS protocol is crucial for maintaining reliable, uninterrupted network communications. As QTS consists of quantum and classical components, potential security vulnerabilities can be in both domains. This paper investigates the vulnerabilities in the classical channel and examines how these weaknesses impact the protocol. An attacker exploiting the weakness in TCP/IP protocol specifically ARP spoofing attack, followed by MITM attack threat is studied. This attacker can alter the timing information exchanged between devices located in respective clocks, resulting in an incorrect time offset calculation in QTS protocol. Simulation is conducted by generating photon detection timestamps following Poisson distribution at each detector and communicating over TCP connection. An attacker is located between two clocks and intercepts the packets. The simulation result illustrates vulnerabilities in the TCP protocol and demonstrates how exploiting these weaknesses can affect clock synchronization accuracy. In addition, TLS protocol is identified as a potential countermeasure mechanism.