A lot of EA is focused on charity evaluation, which involves looking at a charity's strategy and impact and cost-effectiveness. 

But to analyze cost-effectiveness well, you have to understand what the charity is actually trying to do. When the charity's strategy is (1) straightforward and (2) pubicly acceptable, this is easy to do. Give Directly gives folks living in extreme poverty money to make their lives better. You can measure what they do (giving people money) and the output (how happy people are) -- it can be complicated to do the latter, but there is a robust research ecosystem dedicated to that, lots of RCTs and other studies to point to, etc. 

What happens when a charity doesn't have an intelligible-to-nonexperts or public facing strategy? Consider a hypothetical animal welfare charity trying to influence scientific research to be more animal friendly. I've chosen this example specifically because (AFAIK) there are no strongly EA aligned charities trying to do this; I'm not thinking of any group in particular. 

Instead of doing this in an obvious way (telling everyone that they are trying to change scientific practice) they think it's more effective to play some kind of 4D chess. They are planning to ingratiate themselves to scientists, do everything they can to look like insiders, and change the field from the inside. They plan to fund some scientists to do work that harms animals but is less harmful than status quo methods, for example, because they are planning to do some kind of slow-scale modification of practices one step at a time. And because a lot of their staff are scientist themselves, they have a detailed inside knowledge of academia works that feeds into their strategic decisions. 

How does this hypothetical charity talk about their work? There are two problems: 

1. Talking publicly about what they are trying to do is literally antithetical to their strategy. So a random donor or even possibly a charity evaluator who reaches out to them to assess cost effectiveness literally cannot be told the actual mission along which to assess cost effectiveness.
2. Even if they are speaking to someone who can safely be told their actual mission, if that person is not an expert in academic culture, they may not understand why the group has made the decision they have. These decisions rely on a deep knowledge of academia and scientists and how scientists choose what methods they use. It would take a significant amount of time to explain to Average Joe Donor why they have chosen the approach they are taking; time that could be spent focusing on their mission. 

I bring up this problem because I've had it in my work, and I've seen it in the work of others. I know of an EA charity whose long term mission, if discussed publicly, would not be as effective. They can't post on the EA forum about what they are actually trying to do. I won't say who they are or even which part of EA they are in because I don't want to mess things up for them!

The reason I bring this up is that people have criticized charities for having publicly facing messages that don't always align with what the critic thinks is right. This group Vetted Causes (example) is just one recent example of this sort of pattern.

But a lot of the time, these critics are not necessarily well-positioned to understand what is going on. They might not be enough of an insider to know the strategy of the organization, or they might not have enough context on the space the organization operates in to understand the strategic choices made. 

I obviously wish things were different and the world was such we could all have EA transparency norms and do our work well, but it isn't. I'm aware this places the average donor in a difficult position: how can you tell if one of these two things is going on, or if the charity is just bad at it's work? I'm not sure; I definitely don't have great answers here. I would just encourage people to wonder, before they criticize groups whose strategies they don't understand, if they don't really have the full picture.