In Eclipse, breakpoint icons tend to get obscured by other notification icons, like override or quick-fix notifications.
The workaround, as described in this bug comment, is to configure the breakpoint annotation type with additional display properties.
To do so, open General > Editors > Text Editors > Annotations and configure your breakpoint annotations as you see fit:
If you select “Text as: Dashed Box”, you can get something like this (note the dashed box around the method name, indicating a method entry breakpoint):
Not the prettiest solution, but at least that’s one less mild annoyance to deal with.