i wrote a comment about this a while ago. reposted:

1. WW2 destruction and recovery. Around a third of the population was either dead or wounded. The most industrially and agriculturally developed areas (for one Ukraine) were devastated. After the war, USSR was economically and politically isolated, they did not benefit from the Marshall Plan like western europe. USSR invested into the eastern block to rebuild cities and industries there. A capitalist country under such economic and demographic strain would fold in 5 years imho. Later on, there were huge investments into the military industry, including support to socialist revolutions around the world, which put more strain on the economy.
2. Increasing economic complexity. After the war, the amount of commodities/materials/indicators in the economy has increased exponentially. As there was a labour shortage (see point 1.), the economic planning model had to be adjusted to accommodate the capacity of the Gosplan. There was a point where cybernetics was considered, but the idea was dropped for being quite experimental and costly to implement. So instead, a retreat to markets was implemented in the form of Kosygin reforms (profit was created as an indicator, other indicators were simplified etc.).
3. Kruschev and dilution of party goals. During his leadership, Kruschev implemented party reforms that have diluted its class character and down-played importance of struggle (like the anti-Stalin speech for instance). It was one of the issues that flung the party and USSR into a spiral of “reforms for the sake of reforms” rather than analysis them as either a retreat or advancement towards communism.
4. Sabotage and public property misuse (corruption). The limited market reforms + party ideological crisis has created a certain “proto-capitalist” class that mainly consisted of factory managers who often appropriated public property for personal gains. They were the main proponents (as a class) for market reforms, but they only really gain power after Gorbachev’s liberalisation and legalisation of private enterprises. Before Gorbachev, this class was very marginal and could be dealt with anti-corruption measures and modernisation, policies that were proposed by Andropov in 1982.

to conclude, there were no deeply ingrained issues, but a lack of capacity, imposed by the war and global isolation.