In this scenario, there are two computers with a 1Gbps private link.
MongoDB runs on one and the application having problems on the other one.

After a few days of running with roughly 10-15 transactions / seconds, I am getting Timeout errors.

The database replies properly on its host.
The link between the two machine is working properly.

There is no replica set, etc, just a single database.
CPU usage is low, there is plenty of memory; that on both computers
I can't figure out what causes this problem; here is the log:

Exception Info: System.TimeoutException
at MongoDB.Driver.Core.Clusters.Cluster.ThrowTimeoutException(MongoDB.Driver.Core.Clusters.ServerSelectors.IServerSelector, MongoDB.Driver.Core.Clusters.ClusterDescription)
at MongoDB.Driver.Core.Clusters.Cluster+WaitForDescriptionChangedHelper.HandleCompletedTask(System.Threading.Tasks.Task)
at MongoDB.Driver.Core.Clusters.Cluster+<WaitForDescriptionChangedAsync>d__44.MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.Core.Clusters.Cluster+<SelectServerAsync>d__37.MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.Core.Bindings.WritableServerBinding+<GetWriteChannelSourceAsync>d__8.MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.Core.Operations.CreateIndexesOperation+<ExecuteAsync>d__15.MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.OperationExecutor+<ExecuteWriteOperationAsync>d__3`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.MongoCollectionImpl`1+<ExecuteWriteOperationAsync>d__61`1[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089],[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.MongoCollectionImpl`1+MongoIndexManager+<CreateManyAsync>d__9[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()
at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
at MongoDB.Driver.MongoIndexManagerBase`1+<CreateOneAsync>d__7[[System.__Canon, mscorlib, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089]].MoveNext()