The Internet of Things (IoT) is widely known as a revolutionary paradigm that offers communication among different types of devices. The primary goal of this paradigm is to implement efficient and high-quality smart services. It requires a protocol stack that offers different service requirements for inter-communication between different devices. Transmission Control Protocol (TCP) and User Datagram Protocol (UDP) are used as transport layer protocols in IoT to provide the quality of service needed in various IoT devices. IoT encounters many shortcomings of wireless networks, while also posing new challenges due to its uniqueness. When TCP is used in an IoT system, a variety of challenging issues have to be dealt with. This paper provides a comprehensive survey of various issues which arises due to the heterogeneous characteristics of IoT. We identify main issues such as Retransmission Timeout (RTO) algorithm issue, congestion and packet loss issue, header overhead, high latency issue, link layer interaction issue, etc., Moreover, we provide several most probable solutions to the above-mentioned issues in the case of IoT scenarios. RTO algorithm issue has been resolved by using algorithms such as CoCoA, CoCoA+, and CoCoA++. Apart from these, the high latency issue has been solved with the help of a long lived connection and TCP Fast open. Congestion and packet loss issue has been resolved by using several TCP variants such as TCP New Reno, Tahoe, Reno, Vegas, and Westwood.

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