A family of Microsoft relational database management systems designed for ease of use.
The message about "illogical" relationships may be about circular relationships that are most frequently caused by having links on summary tasks (summary to summary) and then adding subtasks and attempting to link them.
Try removing links on the summary tasks (summary to summary). If that doesn't work, it might be worth saving a copy of the file as XML and then re-importing the XML file into a new project. Test and see if that is better.