I have this same problem on sprint model. Happend on zv8, and zva. Usually if I close and restart the browser it works again. I have no fix but it does happen. I also get pop ups in the stock browser alot for sites that have security certificates that say they are invalid. However when I inspect them, they are. The latter happens a ton when browsing XDA actually. Its related to the advertising they use on the site.
Sprint LG G2 >> Current Owner >> Stock, Debloated, Rooted, TWRP'ed
Sprint HTC One >> Current Owner >> Stock, Unrooted (Till Kit Kat Comes)
Sprint Moto Photon >> Current Owner >> Rooted, Docked, Converted to XMBC & Android Media Box
TMO HTC G2 >> Past Owner >> Imo, The best Phone ever made design wise.