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Upon opening the Map Topology dialog box and checking layers in the list to be included in the topology, some of the layers have been unchecked when the dialog box is reopened. In addition, those layers are not affected by any shared feature edits.
Some layers are being projected on the fly.
To participate in a map topology, the projections of all the layers and the data frame need to be the same. This may mean that either the layers need to be reprojected so they match other layers, or the projection of the data frame needs to be changed to match the layers.
Stop the edit session before doing this.