There are two reasons why a group of order $p^a.q^b$ is not a semi-direct product of its Sylow-subgroups. The first case is when the Fitting length is at least three or, said another way, when $G/F(G)$ is not nilpotent with $F(G)$ being the Fitting subgroup. The second case is when $G/F(G)$ is nilpotent with an order multiple of both $p$ and $q$.
In the first case, we must have $(p,q)=(2,3)$, $(p,q)=(3,2)$ or $(p,q)=(3,13)$. There are, according to GAP, 17 suitables groups of order 144 and one group of order 324. GAP is not managing $13689=3^4.13^2$ but, if I'm not mistaken, there are four suitable groups for that order. More precisely, those four groups have a characteristic cyclic subgroup of order 13 with a quotient of order 1053 and of the form $(C_3^3 \rtimes C_{13}) \rtimes C_3$.
In the second case, we have $q=p^2+p+1$ and the group is isomorphic to $(C_p^3 \rtimes C_q) \times (C_q \rtimes C_p)$. According to Bunyakovsky conjecture, this should yield an infinite family of groups.
This answer is based on personnal research, which is not fully completed and not published, so there is risk of errors in it.