This is due to the audio having stereo (left and right) channels being out-of-phase.
To put it very simply, when the audio waveform on the left channel is out-of-phase with the right channel, the resulting mono mix (basically (left+right)/2) may reduce the volume or even mute it (further reading: destructive interference & dead spot).
When playing with headphones or stereo speakers, there should be no issue hearing the audio because each channel is played through each speaker respectively. However, this becomes an issue if the device only supports mono playback (like on some Android devices, including Nexus 5) due to the previously mentioned phenomenon.
Depending on the model, there might be a true stereo (left-right channel separation) mod that can be applied/flashed. E.g. a detailed post by user "chdloc" on XDA Forum to apply true stereo on Nexus 5
The alternative workaround is to fix the audio source by inverting the waveform on one of the channels. Example using Audacity (reference: https://forum.audacityteam.org/viewtopic.php?t=71779):
- Open the audio file
- (Optional) Select the track, then open the menu bar: Tracks - Mix - Mix Stereo Down to Mono to see the effect of destructive interference, then undo the operation to continue to the next step
- Select the track
- Open menu (press Shift + M, or click the dropdown menu above the "Mute" and "Solo" button)
- Select "Split Stereo Track"
- Select one of the channels (either left or right)
- Select all region of the track (double-clicking the waveform, or from the menu bar: Select - Region - Track Start to End)
- On the menu bar, select Effect - Invert
- Open menu on the first track (follow step 4)
- Select "Make Stereo Track"
- (Optional) Select the track again, then open the menu bar: Tracks - Mix - Mix Stereo Down to Mono to see if it is still affected by the destructive interference, then undo the operation to continue to the next step
- Export the resulting audio from File - Export - ...