There were many, many problems with the Maratha polity and Panipat was a symptom rather than the problem itself. One must understand that the Maratha 'state' was severely decentralised- it showed the same problems the Mughal state did, but on an accelerated time scale; ie different sources of authority vested in the Peshwa, Chhatrapati, and the individual bands and Chiefs.

It must also be understood that the Marathas were functioning within an all-India framework. I've used the term Mughal system before, and while Sir Jadunath Sarkar coined itand I would still be weary approaching his work, it is a good term. The Marathas regularly engaged with the Mughals in a way that made them both insiders and outsiders at the same time. It is during this time, for example, that the Shinde of Gwalior becomes Amir ul Amara of the Mughal Emperor; his chief noble. This is a way to actually hold the Mughal hostage. Note the importance of a chief over the state as a whole.

The biggest example of this, however, is the tax regime of the Maratha polity. They essentially levied a second tax on top of Mughal taxes, because they derived their authority from the latter. Their sardeshmukhi was a burden on cultivators, and they had to act as almost raiders to collect this additional fee. The existence of 'chauth', a tax to be submitted to a person rather than the state, added to the problem as it made the Maratha polity individual driven to the detriment of the state.

Outside of Maharashtra, the polity also essentially raided and pillaged without setting up real administrations. Places like Gwalior and Indore were supposed to be temporary arrangements, and the chiefs of those areas wanted to return to Maharashtra ASAP. When that did not come they simply went on to do other things. In many ways, it could be called a form of proto- colonialism as Maharashtra was the metropole, while the rest of India was simply an opportunity to raid for booty and taxes.

This is only a cursory assessment of the problems with the Maratha state, and it heavily leaned on the Cambridge History of the Marathas. If you have access to it it is a great source, and takes the time to address the functions of the Maratha state and how it worked. In lesser words, a lot of the problems with the Marathas are that they were a confederation within a confederation and relied heavily on individual initiative. In a military sense, it was a mess when it came to leadership. In a political sense, it was a mess because of constant jockeying for authority, without a clear hierarchy.

EDIT:

So I mixed up chauth and sardeshmukhi. Chauth was a base tax of a quarter upon which sardeshmukhi was an additional levy. In practice, it was the latter that was usually assigned to a person as a way of tiding them over and gaining favour. So being given sardeshmukhi and even chauth rights was considered a way to gain tangible power within the Maratha state.