We report the discovery and direct visualization of skyrmion clusters with mutually orthogonal orientations of constituent isolated skyrmions in chiral liquid crystals and ferromagnets. We show that the nascent conical state underlies the attracting inter-skyrmion potential, whereas an encompassing homogeneous state leads to the repulsive skyrmion-skyrmion interaction. The crossover between different regimes of skyrmion interaction could be identified upon changing layer thickness and/or the surface anchoring. We develop a phenomenological theory describing two types of skyrmions and the underlying mechanisms of their interaction. We show that isolated horizontal skyrmions with the same polarity may approach a vertical isolated skyrmion from both sides and thus constitute two energetically different configurations which are also observed experimentally. In an extreme regime of mutual attraction, the skyrmions wind around each other forming compact superstructures with undulations. We also indicate that our numerical simulations on skyrmion clusters are valid in a parameter range corresponding to the A-phase region of cubic helimagnets.