Why is there a thin rectangle beneath the launchpad icon in my dock?

You can try this, may help.

Go step by step and test.

1. Restart the computer.

2. Startup into SafeMode

Start up in Safe Mode. http://support.apple.com/kb/PH18760

3. If the steps given above don’t help, try restarting the Dock.

Restarting the Dock:

Applications > Utilities > Terminal

Launch Terminal.

Wait until the $ sign shows up.

Enter the command killall Dock

Press the enter key on the keyboard. Wait until the prompt shows up.

Quit Terminal.

The thin line is a progress bar. If it's not being "filled" the download might have stalled. Restart often clears the issue and/or resumes the download.

Remove the LaunchPad icon from the Dock by dragging it upward. Then open the Applications folder and drag the icon from there back into the Dock. The other icons will move aside to make a space for it.