In EA there are - broadly speaking - two types of stereotype. In very simple terms, one type qualifies a 'standard' UML element type to create a new type of element that represents something from a Technology specification - SysML, TOGAF, ODM, ArcGIS and so on, or for a Technology that has been developed 'in-house'. It was created by the Technology developer. So, don't worry about what the stereotype does, look at what the element or connector is and what the relevant spec defines it as. This stereotype is already in the element when you create it from the toolbox.
The other type of stereotype is simply a label that might or might not also adjust the appearance of the element with an image file, shapescript or just color changes. You apply it to an existing element, and it does not change the element type. Anyone can create them in the UML Types dialog, for any reason. If you have a disciplined team and good guidelines, you can read the stereotype notes in that dialog and see why the stereotype was necessary. At the other extreme, there can be a huge number of stereotypes that have no real purpose other than 'to see what it does', and there might well be several stereotypes with the same name. Don't waste time trying to understand these ones, they don't do more than alter the appearance of the element, and you can easily see that effect.
The actual example you gave illustrates a problem with changing the existing stereotype in an element. Who knows why someone wanted to change the defining stereotype of a SysML Requirement? If the Capability stereotype is just applying different colors, that's OK, the nature and purpose of the element are not changed. However, Capability is a stereotype that defines the Capability Class element type in TOGAF, so if you also have TOGAF enabled, the system applies the TOGAF Capability Class characteristics (as far as it is able) to the SysML Requirement resulting in a strange hybrid.
Basically, if the element is doing what you need it to do, don't worry about the stereotype. If it isn't, see if there is another element type that serves the purpose, or discuss with a Technology Developer your need for that object. If the element stereotype looks 'odd', go and talk to the element author or owner; they are the best person to explain what has happened and why.
