Flags themselves have no operating issues. They provide a very easy and fast way of keeping states during processing a request or during a transcation, if OpenSER is in stateful mode.
One of the main purposes for flags is to enable accounting in OpenSER. The “acc” module uses flags to identify transactions to be accounted. These transactions are usually marked from configuration file using “setflag()” function.
You should know that the local transcations are not processed by configuration file interpreter. The local transactions are usually initiated using OpenSER's FIFO interface, either by a user or another application like SERWEB (click to dial), or SEMS (voicemail, ISDN gateway, ...). Local transaction may also be initiated by OpenSER itself, from some module (msilo, sms/xmpp gateway).
So, the issue is not actually related to flags, but you should know that you can't set flags for local transactions from configuration file. For example, if you account calls to voicemail, and you use SEMS via local FIFO file, you may not get the BYE accounted in the case voicemail system teared down the call. So, if you don't want to keep only the INVITE requests, you can reset the accounting flag just before forwarding to voicemail.