Arc- and tail-like structures associated with disks around Herbig stars are likely a consequence of infall events occurring after the initial collapse phase of a forming star consistent with the observation of luminosity bursts. An encounter event of gas with an existing star can lead to the formation of a second-generation disk significantly after the initial protostellar collapse phase. Additionally, observations of shadows in disks can be well described by a configuration of misaligned inner and outer disk, such that the inner disk casts a shadow on the outer disk. Carrying out altogether nine 3D hydrodynamical models with the moving mesh code AREPO, we test whether a late encounter of an existing star-disk system with a cloudlet of gas can lead to the formation of an outer disk that is misaligned with respect to the primordial inner disk. Our models demonstrate that a second-generation disk with large misalignment with respect to an existing primordial disk can easily form if the infall angle is large. The second-generation outer disk is more eccentric, though the asymmetric infall also triggers eccentricity of the inner disk in the range of 0.05 to 0.1. Retrograde infall can lead to the formation of counter-rotating disks and enhanced accretion. As the angular momentum of the inner disk is reduced, the inner disk shrinks and a gap forms between the two disks. The resulting misaligned disk system can survive for 100 kyr or longer without aligning each other even for low primordial disk masses given an infall mass of 0.01 % of a solar mass. Synthetic images of our models reveal shadows in the outer disk similar to the ones observed in multiple transition disks that are caused by the misaligned inner disk. At large enough radius, the dust located in the shadow region has lower temperature possibly leaving observational traces. We conclude that late infall events can be responsible for observations of shadows in at least some transition disks.