Java: `getLocation()` result contains same location twice for some elements

### Description
For some elements the result of `getLocation()` contains the (seemingly) same location twice. Absolute file path, line and column numbers all seem to match, but for some reason these are two separate `Location` entities.

(Note that there are also other cases where `getLocation()` has more than one result, but at different locations, see #5734 and #7309. However, the issue described here appears regardless of whether the project has multiple modules / sub-projects or not.)

### Example query
```ql
import java

from Top t
where
// Only consider results in source code
t.getLocation().getFile().getExtension() = "java"
// And there are at least two different Location elements
and exists(Location location, Location otherLocation |
location = t.getLocation()
and otherLocation = t.getLocation()
and location != otherLocation
|
// Only consider if in same file; ignore if file is present multiple times with different paths, see #5734
location.getFile().getAbsolutePath() = otherLocation.getFile().getAbsolutePath()
)
// Only consider if all locations are exactly the same
and count(t.getLocation().toString()) = 1
select t, t.getLocation()
```
[Query Console link](https://lgtm.com/query/3705892995164895283/)