diff --git a/common/include/villas/graph/directed.hpp b/common/include/villas/graph/directed.hpp
index cd75102dd..506d87012 100644
--- a/common/include/villas/graph/directed.hpp
+++ b/common/include/villas/graph/directed.hpp
@@ -42,7 +42,7 @@ public:
 
 	std::shared_ptr<VertexType> getVertex(VertexIdentifier vertexId) const
 	{
-		if (vertexId >= lastVertexId)
+		if (vertexId >= vertices.size())
 			throw std::invalid_argument("vertex doesn't exist");
 
 		// cannot use [] operator, because creates non-existing elements
@@ -154,6 +154,7 @@ public:
 
 				auto startVertex = getVertex(edge->from);
 				startVertex->edges.remove(edge->id);
+
 			}
 
 			if ((edge->from == vertexId) or removeEdge) {
@@ -167,6 +168,7 @@ public:
 
 		logger->debug("Remove vertex {}", vertexId);
 		vertices.erase(vertexId);
+		lastVertexId--;
 	}
 
 	const std::list<EdgeIdentifier>&
diff --git a/common/lib/kernel/vfio_container.cpp b/common/lib/kernel/vfio_container.cpp
index e0c36421b..6c301eb77 100644
--- a/common/lib/kernel/vfio_container.cpp
+++ b/common/lib/kernel/vfio_container.cpp
@@ -93,11 +93,10 @@ Container::Container() :
 
 Container::~Container()
 {
-	log->debug("Clean up container with fd {}", fd);
-
 	/* Release memory and close fds */
 	groups.clear();
 
+	log->debug("Cleaning up container with fd {}", fd);
 	/* Close container */
 	int ret = close(fd);
 	if (ret < 0)
diff --git a/common/lib/kernel/vfio_device.cpp b/common/lib/kernel/vfio_device.cpp
index 568921759..a5f59564f 100644
--- a/common/lib/kernel/vfio_device.cpp
+++ b/common/lib/kernel/vfio_device.cpp
@@ -125,11 +125,14 @@ Device::Device(const std::string &name, int groupFileDescriptor, const kernel::p
 
 Device::~Device()
 {
-	log->debug("Clean up device {} with fd {}", this->name, this->fd);
+	log->debug("Cleaning up device {} with fd {}", this->name, this->fd);
 
 	for (auto &region : regions) {
 		regionUnmap(region.index);
 	}
+	if (isVfioPciDevice()) {
+		pciHotReset();
+	}
 	reset();
 
 	int ret = close(fd);
@@ -412,6 +415,7 @@ bool Device::pciHotReset()
 	if (!isVfioPciDevice())
 		return false;
 
+	log->debug("Performing hot reset.");
 	const size_t reset_info_len = sizeof(struct vfio_pci_hot_reset_info) +
 	                              sizeof(struct vfio_pci_dependent_device) * 64;
 
@@ -461,7 +465,7 @@ bool Device::pciHotReset()
 	delete[] reset_buf;
 
 	if (!success) {
-		log->warn("PCI hot reset failed, maybe not IOMMU available?");
+		log->warn("PCI hot reset failed, maybe no IOMMU available?");
 		return true;
 	}
 
diff --git a/common/lib/kernel/vfio_group.cpp b/common/lib/kernel/vfio_group.cpp
index bac909768..b17b4a25e 100644
--- a/common/lib/kernel/vfio_group.cpp
+++ b/common/lib/kernel/vfio_group.cpp
@@ -118,11 +118,11 @@ void Group::dump()
 
 Group::~Group()
 {
-	log->debug("Clean up group {} with fd {}", this->index, this->fd);
-
 	/* Release memory and close fds */
 	devices.clear();
 
+	log->debug("Cleaning up group {} with fd {}", index, fd);
+
 	if (fd < 0)
 		log->debug("Destructing group that has not been attached");
 	else {