GiveWell and Life You Can Save have different evaluation methods. @The Life You Can Save describes their evaluation framework here. @GiveWell explains theirs here.
From my quite ignorant outsider view, the difference seem to be:
1. GiveWell aims to find the most cost-effective charities based on calculations of cost-per-life-saved or cost-per-economic-benefit. The Life You Can Save seems to consider these sorts of calculations to be too uncertain and dependent on subjective assumptions to allow for charities to be ranked reliably, so they recommend an unranked collection of generally very good charities. The Life You Can Save says that they...
do not try to claim that an intervention or the organization that implements it is the most cost-effective. We consider that cost-effectiveness calculations are built on subjective valuations such as the value of life at different ages, the extent of suffering alleviated by a given intervention, and our best guesses about recipient utility and preferences. Small changes in many of these underlying assumptions can lead to widely differing answers. Our goal is to provide donors assurance that giving money to an organization is a great bet, highly likely to do good, and cheap enough to be scalable, durable, and/or have a deep impact on people’s lives
2. GiveWell is more hard-line about gaps in evidence being disqualifying. With the example of Fred Hollows, GiveWell says:
Our analysis is limited by the fact that we have not yet identified high quality estimates of the cost of providing an additional cataract surgery. We had conversations with 17 organizations that work to expand access to cataract surgery and we concluded that it would be costly to measure or estimate how many additional surgeries each of these organizations cause to happen that would not have happened in the absence of its work
The Life You Can Save seems to be more willing to accept gaps in the evidence as long as some good evidence exists and the charity fits other, softer criteria, like how convincing their theory of change is (explained in their long and sort of convoluted evaluation framework). For this reason they do recommend Fred Hollows.
TL;DR: In sticking to hard evidence and cost-effectiveness calculations, GiveWell is potentially leaving behind highly effective charities whose effectiveness is harder to prove or producing questionable rankings because of questionable assumptions, while The Life You Can Save's more holistic evaluation approach is potentially including charities whose evidence has holes in it and they draw no distinction in quality between Malaria Consortium and the Fred Hollows Foundation, even though a substantial difference in effectiveness might exist