Assume P != NP. Then there are many examples of problems in NP that are known not to be NP-complete, like 2-SAT, and many that are conjectured not to be NP-complete, like factorization. However, are there any problems that are widely conjectured but not known to be NP-complete?
There are no natural problems that I am aware of that have that property. There are two problems which are "close", however.
The Minimum Circuit Size Problem is, given a truth table of a boolean function $f$ and an integer $k$, is $f$ computed by a circuit of size at most $k$? Note $MCSP \in NP$, and it is widely expected that $MCSP$ is "hard"; however, it is not known that $MCSP$ is $NP$-complete, and while it is easy to conjecture that it might be, there is also some evidence that it is not.
The Unique Games Conjecture states that approximating the value of a certain combinatoric problem is $NP$-hard. This problem is not strictly in $NP$ because its decision version is a "promise problem". Nevertheless, the UGC is one of the premier open questions of computer science today and there is little consensus on whether it is true or not.