I was having the same issue and managed to solve it by modifying some offending lines in the project file via a text editor.
The main thing that led me to the solution of this problem was the error message from the report;
Tried to access the containerPortal of an orphaned container item proxy. A common cause of this is corrupt project files which illegally reuse the same target dependency instance for multiple targets.
To fix this problem just follow my instructions below but ensure that xcode is closed before continuing.
Firstly, open the project container (go to finder, and do 'show package contents' on the xcodeproj file).
At this point based on some advice from another thread I cleared out all of the workspace settings and left nothing except the "pbxproj" file to be on a blank slate (I am not 100% sure if that was necessary, but it didn't hurt since the only things you lose are breakpoint locations, windows and tab locations, etc.).
Next, open the pbxproj file in a text editor and look for the word 'dependency'. This should lead you to a part of the file that says something like:
/* Begin PBXNativeTarget section */
Below that you should see a section with all your targets listed. In my case I had my MainProject and my MainProject-cal targets, where I was trying to delete the MainProject-cal. In the error message it notes the use of the same dependency in multiple targets being a problem so I looked through. Here's what it looked like for me before I made any changes:
/* Begin PBXNativeTarget section */
xxxx /* MainProject */ = {
...
dependencies = (
A /* PBXTargetDependency */,
B /* PBXTargetDependency */,
C /* PBXTargetDependency */,
);
...
xxxx /* MainProject-cal */ = {
...
dependencies = (
D /* PBXTargetDependency */,
B /* PBXTargetDependency */,
F /* PBXTargetDependency */,
);
...
/* End PBXNativeTarget section */
(I simplified the hex into x's or single characters, and stripped out some extra stuff for readability)
So if you look based on my above excerpt you'll notice that the dependency 'B' appears both in the MainProject and MainProject-cal. In the dependencies of MainProject-cal I simply removed the offending line (e.g. cut out the line labelled 'B'), saved the file, and started Xcode again. At that point, when I tried to remove the target everything worked fine and Xcode didn't crash. Problem solved! Hope that helps - I've been wrestling with this issue for weeks.