Grids, Levels and Reference Planes are all considered datum elements within the Revit database, meaning that they can be used by other elements to drive geometry. For this reason they should be carefully reviewed as your project progresses using Ideate Explorer.
Grid lines can become duplicated, via Copy/Monitor or other methods such that there are two copies of a Grid line that exist in the same file and in the same location. Once this happens it will prevent that grid number from being able to be used and may also result in other unintended results. Use Ideate Explorer to quickly review the list of Grids. For any suspect Grid name, simply double-click on the Grid instance to open a view where it can be viewed. Once selected it can be moved or deleted using Revit methods.
Level lines, when deleted, will take certain hosted elements with them, without warning. This is the primary cause of mysteriously deleted Revit elements. For this reason the model manager needs to keep a very tight reign on Levels. Use Ideate Explorer to look for any newly created Level lines AND to carefully move elements that have been placed on an incorrect Level (before the level can be safely deleted).
To move elements from one level to another using Ideate Explorer:
TIP: In-place families will not have a Level.
Unnamed reference planes are a visual distraction and make selection difficult. Use Ideate Explorer to quickly delete all unnamed reference planes.