You should re-evaluate the file naming convention you are using and also re-evaluate the way your files are being stored. Instead of allowing overwriting of duplicate names, your software is appending the .1 to the duplicate name file.
There are different ways to use Lightroom, as far as exactly how files are ingested; where they go, how they are named or re-named, etc.. Some people llow Lightroom to automatically ingest images as soon as a memory card is inserted into the card reader, and they allow Lightroom to work in its automated manner. Others, like me, MANUALLY transfer files from card readers into individually-created folders, using a simple date system, and then we manually "point" Lightroom to those folders, and manually drill down and then manually tell Lightroom to Import the files.
As far as the file being partially corrupted: I have had that problem on multiple occasions, where ONE, single file will cause an issue.
Lightroom is a regal PITA when files, or their folders, are re-named...this is I think, one of the weaker aspects of the app.