The blistering of elastic membranes is prone to elastic-solid as well as substrate-based mechanical instabilities. The solid-based instabilities have been well-explored in the mechanically indented blisters of elastic membranes over the rigid/solid substrates, but an integrated study illustrating the underlying mechanism for the onset of solid as well as substrate-based instabilities in the spontaneous blistering of a 2D material is still lacking in the literature. In this article, an extensive experimental as well as analytical analysis of the spontaneous blister-formation in the multilayer graphene (MLG) flakes over a polymeric substrate is reported, which elucidates the involved mechanism and the governing parameters behind the development of elastic-solid as well as viscoelastic-substrate based instabilities. Herein, a 'blister-collapse model' is proposed, which infers that the suppression of the hoop compression, resulting from the phase-transition of the confined matter, plays a crucial role in the development of the instabilities. The ratio of blister-height to flake-thickness is a direct consequence of the taper-angle of the MLG blister and the thickness-dependent elasticity of the upper-bounding MLG flake, which shows a significant impact on the growth-dynamics of the viscous fingering pattern (viscoelastic-substrate based instability) under the MLG blister.