why was it that some of the farm work was not being done as efficiently as previously?

I think they were exhausted but Chapter 6 outlines both efficiencies as well as shortages. Check out this quote from Chapter 6.

The animals were not badly off throughout that summer, in spite of the hardness of their work. If they had no more food than they had had in Jones's day, at least they did not have less. The advantage of only having to feed themselves, and not having to support five extravagant human beings as well, was so great that it would have taken a lot of failures to outweigh it. And in many ways the animal method of doing things was more efficient and saved labour. Such jobs as weeding, for instance, could be done with a thoroughness impossible to human beings. And again, since no animal now stole, it was unnecessary to fence off pasture from arable land, which saved a lot of labour on the upkeep of hedges and gates. Nevertheless, as the summer wore on, various unforeseen shortages began to make them selves felt. There was need of paraffin oil, nails, string, dog biscuits, and iron for the horses' shoes, none of which could be produced on the farm. Later there would also be need for seeds and artificial manures, besides various tools and, finally, the machinery for the windmill. How these were to be procured, no one was able to imagine.