Some questions related to free-by-cyclic groups and tubular groups

We prove that a CAT(0) free-by-cyclic tubular group with one vertex is virtually special, but many of them cannot virtually act freely and cocompactly on CAT(0) cube complexes. This partially confirms a question of Brady--Soroko \cite[Section 9: Question 1]{BS} and answers a question of Lyman \cite[Question 1]{Ly} in the negative. Furthermore, we provide examples of free-by-cyclic groups amalgamated along cyclic subgroups that are not virtually free-by-cyclic. This answers negatively a question of Hagen--Wise \cite[Remark 3.6]{hw}. Lastly, we exhibit an example of a cyclic-subgroup-separable tubular group that does not have the property (VRC) (i.e. every cyclic subgroup is a virtual retract). This answers a question of Minasyan \cite[Question 11.6]{min} in the negative.