Despite owners Fenway Sports Group wiping out debts of £200m with their October 2010 purchase of the club, they had to write off a further £35m associated with the doomed HKS-designed Stanley Park project of predecessors Tom Hicks and George Gillett.
And Hodgson's exit in January 2011, after just 191 days in charge, and the departure of former managing director Christian Purslow, contributed to a further £8.4m relating to contract terminations, accounts filed to Companies House show.
Current managing director Ian Ayre insists the accounts, without that "extraordinary" expenditure, are in good shape.
"I guess people will focus on the loss of £49.4m and there's no business - or people running any business - who are going to be pleased with any loss," he told the Liverpool Echo.
"But I think the important indicator here is this £59m charge for exceptional items and as a business that's been in a transition, it's about moving from where we were to where we want to be.
"We have written off a huge amount on the stadium project. A big chunk of that £50m loss relates to the HKS project - which is now defunct - and associated costs around that."
Following their takeover in 2007, Hicks decided to abandon established plans for a new ground in Stanley Park and engaged Dallas-based architects HKS, who came up with an ambitious glass and steel design.
Soon after taking over, FSG scrapped that project but there were still residual costs associated with legal, planning and design fees, which needed to be settled and resulted in a huge deficit.
"With new ownership that was kind of milling around within the club's accounts and there was a very definite need to move that out," said Ayre.
"It is a huge loss but that goes with a lot of other things that nobody was really happy with in that period.
"So rather than dwell on it, we've very smartly made the decision to remove it from the club's accounts.
"It is a big write-off but it means that it's gone forever now and we can move forward now without that around our neck.
"And it also means that we are in pretty good shape in being a sustainable business. It's a positive step forward."
Ayre insisted the amount of money spent on contract terminations was less unusual, although dispensing with Hodgson after six months in charge was out of the ordinary for Liverpool, who have a history of sticking with managers for much longer.
"It's nothing untypical of anything in football. Contracts are typically fixed term," said Ayre of the pay-offs.
"When you make a decision to terminate somebody, the right and proper thing to do is honour the pay-out of that contract.
"This relates to Roy and to some of his backroom staff and also to Christian Purslow leaving. It's standard across football.
"It's unfortunate to have to have them - nobody wants to see anybody go - but in certain circumstances it's right to make a change and that's what that relates to."
On the accounts as a whole Ayre said they were in better shape long-term as a result of the action taken by the owners.
The figures do not include the kit deal signed with American company Warrior Sports, which is worth at least £25million a year.
"If we had not written off these extraordinary costs, we would have been looking at breaking even," Ayre said.
"We have reduced interest charges from £18m to about £3m. That puts us in a much stronger position to utilise our revenues more effectively on the team.
"These figures in many ways represent the commitment of the owners, in paying down the acquisition debts and in other areas.
"What is reflected in these accounts was going on around the time they actually came into the club.
"It's not where we are today. It's a year on, so it was a big commitment at an early stage
"The owners have continued to make changes and commitments.
"They have made some great investment at the start; they cleaned up a lot of what was a problem at Liverpool and they have invested in both the team on and off the pitch.
"They continue to do that and look at what's right - and what works and what doesn't work."