It's not an issue. The oneagent daemon (the part that runs as separate processes) does not affect deep monitoring.
Deep monitoring is activated on the application startup by preloading the liboneagent.so library to every process. This activation is independent from the start of the Oneagent daemon. The only case I can think of would be that the agent was removed or switched to infrastructure mode when agents were restarted.
If some applications are not instrumented, try inspecting the logs and inspect the /etc/ld.so.preload.