I've successfully designed a multi-band frequency-reconfigurable antenna. However, after simulation, I found that the gain is negative. Considering that I'm using a lumped port, where exactly could the issue be?
The gain could be negative. Possible causes include antenna type (where in the radiation pattern are you checking the gain), losses (due to mismatch, material, passive/active components), or mutual coupling. Would be difficult to pinpoint the cause without details of your design.
Negative gain in dB (or probably dBi) means that it radiates less in that direction than an imaginary reference omnidirectional or isotropic antenna would. -1 dB means about 80%, -3 dB means about 50%. An imaginary reference omnidirectional antenna radiates all the input power evenly in all directions. This is defined to have a gain of 1 in all directions, which is 0 dBi (i means isotropic).
If you have negative gain you may not have successfully designed a multi-band frequency-reconfigurable antenna. It depends on whether good gain was a requirement. Antennas are usually made reconfigurable so that they have useable gain at each frequency and/or direction chosen. Good gain means longer battery life and/or longer range and/or higher data rate.