Endohedral metallofullerenes (EMFs) are sub-nano carbon materials with diverse applications, yet their formation mechanism, particularly for metastable isomers, remains ambiguous. The current theoretical methods focus mainly on the most stable isomers, leading to limited predictability of metastable ones due to their low stabilities and yields. Herein, we report the successful isolation and characterization of two metastable EMFs, Sc₂C₂@C₁(39656)-C₈₂ and Sc₂C₂@C₁(51383)-C₈₄, which violate the isolated pentagon rule (IPR). These two non-IPR EMFs exhibit a rare case of planar and pennant-like Sc₂C₂ clusters, which can be considered hybrids of the common butterfly-shaped and linear configurations. More importantly, the theoretical results reveal that despite being metastable, these two non-IPR EMFs survived as the products from their most stable precursors, Sc₂C₂@C_2v(5)-C₈₀ and Sc₂C₂@C_s(6)-C₈₂, via a C₂ insertion during the post-formation annealing stages. We propose a systematic theoretical method for predicting metastable EMFs during the post-formation stages. The unambiguous molecular-level structural evidence, combined with the theoretical calculation results, provides valuable insights into the formation mechanisms of EMFs, shedding light on the potential of post-formation mechanisms as a promising approach for EMF synthesis.