Sure, and this mainly came to my attention b/c their chapters jumped ahead on a series I currently follow. To me, watermarks negatively affect quality as does interrupting a chapter for site referrals. Mangadex coincidentally has a "report chapter" feature with an option being "watermarked...
ManhwaFreak's recent uploads left me wondering about this site's policy on watermarks. Take their latest chapter of L.A.G. as an example; there are 9 banner watermarks that overlay panels and 8 reminders to view on their website between. Is this an issue?