Extra frequencies after applying low pass filter
The issue is that you're violating Nyquist which requires that the sampling rate be at least twice the rate of the highest frequency in the signal. In your case all of the sines that you're generating above 5000 Hz are folding back. For example, a 5100 Hz tone (5000+100) would fold back to 4900 Hz (5000-100) and so on.

The 1 kHz tone you highlighted is the 9 kHz tone you generated, but folded back. If you look at your graph more closely you'll notice that this tone is in the unfiltered signal and is in no way related to the filtering.