When placing a Illustrator file in Indesign, the Illustrator file sometime changes from 100%. When you select the placed file with the selection tool, it says 100%, but if you select with the direction tool, file has been changed any where from 98 to 102 %, not staying at the 100%? why is this and how can you asure the size does not change when placed or when updating the illustrator link?
The Selection tools shows the scale of the frame, and reverts to 100% if your preferences are set to "apply to content." The Direct Select tool always shows the actual scale of the content of the frame.
There is also a preference for relinking that lets you choose between preserving the scale and preserving the dimensions of the linked content.
However, if you edit an illustrator file and your crop options were set to bounding box or art, there's a good chance the size of either of those boxes has changed if anything was deleted or moved, so it is very likely that the scale factor would change on update.
Probably you have inserted files in a frame whose content was previously adequate with "Fit Content Proportionally" or "Fill Frame Proportionally".
The new content in the same frame will have the same characteristics as the previous one