Recently, Belle collaboration reported remarkable observations, cross section for exclusive production of $J/Ψ+η_c$ in $e^{+} e^{-}$ annihilation, a new narrow resonance X(3872) in $B→(J/Ψππ)K$ decay channel. Measurements of the cross section for exclusive $J/Ψ+η_c$ and inclusive $J/Ψ$ production by Belle collaboration differ substantially from theoretical predictions, till now has not been explained conclusively. Given the observed final state and the observed mass, it is natural to assume that the X(3872) is itself a charmonium state. It has however proved difficult to interpret X(3872) as narrow $c \\bar c$ mesons, the quantum number of X(3872) has not been uniquely determined. As another important issue in charmonium physics, $J/Ψ$ and Ψ`` polarization measurement at high $p_T$ by CDF collaboration at the Fermilab Tevatron has been in large deviation from prediction based on color-octet mechanism of NRQCD, which predict almost transverse polarization at high $p_T$. This is the most serious challenge to the NRQCD factorization approach. In this thesis, first as the economic way to identify origin of remarkable discrepancy in the cross section of $J/Ψ+η_c$ or inclusive $J/Ψ$ production, inclusive production of four charm hadrons in $e^+ e^-$ annihilation is studied. Also it is shown that as a phenomenological model for inclusive quarkonium production color-evaporation model (CEM) predict that the inclusive $J/Ψ$ production cross section is even smaller than the NRQCD prediction, so the Belle measurements. Second, using chiral lagrangian approach we study dipion invariant mass spectrum in $X(3872) → (J/Ψππ)$ which is useful to probe nature of X(3872). Finally, by notifying that the soft gluons around color-octet produced $c \\bar c$ or parental hard gluon could be hadronized into multi pions, it is argued that color-octet mechanism does not necessarily imply that $J/Ψ$ or Ψ`` polarization should be almost transverse.